Patterned progression of bacterial populations in the premature infant gut

In the weeks after birth, the gut acquires a nascent microbiome, and starts its transition to bacterial population equilibrium. This early-in-life microbial population quite likely influences later-in-life host biology. However, we know little about the governance of community development: does the gut serve as a passive incubator where the first organisms randomly encountered gain entry and predominate, or is there an orderly progression of members joining the community of bacteria? We used fine interval enumeration of microbes in stools from multiple subjects to answer this question. We demonstrate via 16S rRNA gene pyrosequencing of 922 specimens from 58 subjects that the gut microbiota of premature infants residing in a tightly controlled microbial environment progresses through a choreographed succession of bacterial classes from Bacilli to Gammaproteobacteria to Clostridia, interrupted by abrupt population changes. As infants approach 33–36 wk postconceptional age (corresponding to the third to the twelfth weeks of life depending on gestational age at birth), the gut is well colonized by anaerobes. Antibiotics, vaginal vs. Caesarian birth, diet, and age of the infants when sampled influence the pace, but not the sequence, of progression. Our results suggest that in infants in a microbiologically constrained ecosphere of a neonatal intensive care unit, gut bacterial communities have an overall nonrandom assembly that is punctuated by microbial population abruptions. The possibility that the pace of this assembly depends more on host biology (chiefly gestational age at birth) than identifiable exogenous factors warrants further consideration.The vertebrate digestive system hosts a profound transition from a state of complete or near-sterility in utero to dense bacterial colonization within weeks of birth. This event has lasting effects on the host (1), influencing health and development (2–4), infection resistance (5, 6), predisposition to inflammatory (7) and metabolic disorders (8), and immune function (9), but remarkably little is known about this process. Gut colonization has been partly characterized in term infants (10–12) who reside in open venues, and who will, therefore, experience many exposures (e.g., contact with older children, adults, and pets, varying diets, oral antibiotics) that could drive microbial population assembly (1, 11–13).A delineation of the dynamics of the natural de novo assembly of this microbial community would form a basis for better understanding how the gut acquires its founding microbiome, and how the bacteria in the gut start their transition to population equilibrium (1, 14, 15). In view of the importance of bacterial gut colonization, we sought to determine if the initial assembly of host intestinal microbial populations follows discernible patterns, and if interventions such as antibiotics or nutrition alter this progression. A discernibly patterned progression would suggest that host biology influences bacterial community assembly more than do random encounters of individuals with microbes, whereas stochastic assembly would suggest that random encounters sculpt population structure. In this latter scenario, the gut serves as a passive culture chamber. Fine interval enumeration of gut contents from multiple subjects in as controlled an environment as possible is needed to answer this question.Here, we demonstrate that the gut microbiota of premature infants residing in a tightly controlled environment of a neonatal intensive care unit (NICU) progresses through a choreographed succession of bacterial classes from Bacilli to Gammaproteobacteria to Clostridia interrupted by abrupt population changes. The rate of assembly is slowest for the most premature of these infants.     

The pathogen Batrachochytrium dendrobatidis disturbs the frog skin microbiome during a natural epidemic and experimental infection

Symbiotic microbial communities may interact with infectious pathogens sharing a common host. The microbiome may limit pathogen infection or, conversely, an invading pathogen can disturb the microbiome. Documentation of such relationships during naturally occurring disease outbreaks is rare, and identifying causal links from field observations is difficult. This study documented the effects of an amphibian skin pathogen of global conservation concern [the chytrid fungus Batrachochytrium dendrobatidis (Bd)] on the skin-associated bacterial microbiome of the endangered frog, Rana sierrae, using a combination of population surveys and laboratory experiments. We examined covariation of pathogen infection and bacterial microbiome composition in wild frogs, demonstrating a strong and consistent correlation between Bd infection load and bacterial community composition in multiple R. sierrae populations. Despite the correlation between Bd infection load and bacterial community composition, we observed 100% mortality of postmetamorphic frogs during a Bd epizootic, suggesting that the relationship between Bd and bacterial communities was not linked to variation in resistance to mortal disease and that Bd infection altered bacterial communities. In a controlled experiment, Bd infection significantly altered the R. sierrae microbiome, demonstrating a causal relationship. The response of microbial communities to Bd infection was remarkably consistent: Several bacterial taxa showed the same response to Bd infection across multiple field populations and the laboratory experiment, indicating a somewhat predictable interaction between Bd and the microbiome. The laboratory experiment demonstrates that Bd infection causes changes to amphibian skin bacterial communities, whereas the laboratory and field results together strongly support Bd disturbance as a driver of bacterial community change during natural disease dynamics.Symbiotic interactions between microbes and multicellular organisms are ubiquitous. In recent years, research to understand the complex microbial communities living in or on multicellular organisms (termed the microbiome) has sparked fundamental changes in our understanding of the biology of metazoans (1–5). The microbiome can affect host health directly by influencing metabolism (6), development (7), inflammation (8), or behavior (9), but it may also influence host health indirectly through interactions with infectious pathogens. The microbiome may interact with pathogens through competition for resources, release of antimicrobial compounds, contact-dependent antagonism, or modulation of the host immune response (10), and an “imbalanced” microbiome may leave the host more susceptible to pathogen infection (11, 12). At the same time, an invading pathogen may disrupt the microbiome (10, 13–15). Thus, the microbiome may play a role in disease resistance, or may itself be disturbed or altered by invading pathogens. Although a wealth of recent research has described associations between microbiome composition and a variety of syndromes in both humans and animals (16–25), documentation of microbiome responses to natural epidemics of known infectious pathogens is rare.Chytridiomycosis is an emerging infectious disease of amphibians caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd). Bd is an aquatic fungus that infects the skin of amphibians and disrupts osmoregulation, a critical function of amphibian skin (26). Chytridiomycosis can be fatal, and the severity of disease symptoms has been linked to Bd load, which is a measure of the density of Bd cells infecting the host (27, 28). Bd has a broad host range spanning hundreds of amphibian species, and has been implicated in population extinctions and species declines worldwide (29–34). Efforts to understand and mitigate the effects of Bd have led to research examining the potential for symbiotic bacteria to increase resistance to infection by the pathogen (35, 36). Bacterial species isolated from the skin of amphibians have been shown to inhibit the growth of Bd and other fungal pathogens in culture (37–39), possibly by producing antifungal metabolites (40, 41). In a controlled laboratory experiment, inundation of Rana muscosa with the bacterium Janthinobacterium lividium protected frogs from subsequent Bd infection (42). These and other studies highlight the possible role of bacteria in resistance to chytridiomycosis, but critical questions remain. First, most research has focused on the ability of cultured bacteria to prevent Bd infection, whereas very little is known about whether Bd infection alters the diverse skin microbiome. Examining this latter concept is critical both to a basic understanding of how the microbiome interacts with pathogens and to conservation efforts because Bd-induced perturbations of the microbiome could undermine attempts to mitigate effects of Bd infection through augmentation with particular bacteria. A second knowledge gap is the paucity of comprehensive culture-independent assessments of the amphibian microbiome, which are important because the vast majority of environmental and symbiotic microbes are not readily cultured, and culture-based methods can lead to severe underestimates of diversity and biased assessment of community composition (43). Few studies have applied next-generation sequencing methods to characterize the microbial communities on amphibian skin (44–47), and, to our knowledge, none have done so in the context of Bd infection. A final challenge to understanding interactions between Bd and bacteria stems from the difficulties of drawing direct connections between laboratory and field studies. Laboratory studies are essential for definitive identification of cause and effect. However, complex natural microbiomes can be impossible to recreate in the laboratory, and field studies are needed to show whether processes identified in the laboratory are relevant in nature.We present paired laboratory and field studies using high-throughput 16S amplicon pyrosequencing both to document associations between Bd infection and the amphibian skin bacterial microbiome in nature and to deduce causal relationships in an experiment. Our work centers on the Sierra Nevada yellow-legged frog, Rana sierrae, which is severely threatened by, and has already suffered drastic declines due to, Bd (28, 48). We surveyed frogs from four distinct R. sierrae populations to test if differences in skin bacterial communities are associated with the intensity of pathogen infection. We then conducted a laboratory experiment to establish causal relationships underlying Bd-bacterial community associations. The data establish a strong effect of Bd infection on the composition of the amphibian skin bacterial microbiome that is consistent between the laboratory experiment and naturally occurring Bd dynamics in wild frog populations.     

Composition of the gut microbiota modulates the severity of malaria

Plasmodium infections result in clinical presentations that range from asymptomatic to severe malaria, resulting in ∼1 million deaths annually. Despite this toll on humanity, the factors that determine disease severity remain poorly understood. Here, we show that the gut microbiota of mice influences the pathogenesis of malaria. Genetically similar mice from different commercial vendors, which exhibited differences in their gut bacterial community, had significant differences in parasite burden and mortality after infection with multiple Plasmodium species. Germfree mice that received cecal content transplants from “resistant” or “susceptible” mice had low and high parasite burdens, respectively, demonstrating the gut microbiota shaped the severity of malaria. Among differences in the gut flora were increased abundances of Lactobacillus and Bifidobacterium in resistant mice. Susceptible mice treated with antibiotics followed by yogurt made from these bacterial genera displayed a decreased parasite burden. Consistent with differences in parasite burden, resistant mice exhibited an elevated humoral immune response compared with susceptible mice. Collectively, these results identify the composition of the gut microbiota as a previously unidentified risk factor for severe malaria and modulation of the gut microbiota (e.g., probiotics) as a potential treatment to decrease parasite burden.Infection by Plasmodium species remain a global health burden causing over 200 million cases of malaria and around 1 million deaths annually, with the vast majority of fatalities being children under the age of 5 y living in sub-Saharan Africa (1). Many Plasmodium infections are either asymptomatic or cause only mild malaria. However, some infections progress to severe malaria that most often manifests as impaired consciousness (cerebral malaria), respiratory distress, and severe anemia (2). The best correlate of disease severity following Plasmodium falciparum infection in humans is parasite density (3, 4).The gut microbiota has an impact on multiple facets of host physiology (5), including shaping susceptibility to numerous diseases (6–14). The effects of the gut microbiota on the host are strongly influenced by the collective composition of the bacterial populations (15), and commensal florae are known to affect local pathogen burdens and host immunity (16–18). In addition to influencing local gut immunity, the gut microbiome affects host immunity to extragastrointestinal tract viral infections (19).Recent studies also support that the gut microbiome modulates Plasmodium infections in humans. Anti–α-gal Abs, induced by the gut pathobiont Escherichia coli O86:B7, cross-react with sporozoites from human and rodent Plasmodium species that impair transmission of the parasite between the vector and vertebrate host; however, this cross-reactive immunity did not affect blood stage parasite burden (20). Additionally, the stool bacteria composition of Malian children correlated prospectively with risk of P. falciparum infection, but not progression to febrile malaria (21). Importantly, it remains unclear whether the gut microbiome also contributes to the development of severe malaria. Using the murine model of malaria, these data demonstrate that the gut microbiome affects blood stage parasite burden and the subsequent severity of malaria.     

Structure,variation, and assembly of the root-associated microbiomes of rice

Plants depend upon beneficial interactions between roots and microbes for nutrient availability, growth promotion, and disease suppression. High-throughput sequencing approaches have provided recent insights into root microbiomes, but our current understanding is still limited relative to animal microbiomes. Here we present a detailed characterization of the root-associated microbiomes of the crop plant rice by deep sequencing, using plants grown under controlled conditions as well as field cultivation at multiple sites. The spatial resolution of the study distinguished three root-associated compartments, the endosphere (root interior), rhizoplane (root surface), and rhizosphere (soil close to the root surface), each of which was found to harbor a distinct microbiome. Under controlled greenhouse conditions, microbiome composition varied with soil source and genotype. In field conditions, geographical location and cultivation practice, namely organic vs. conventional, were factors contributing to microbiome variation. Rice cultivation is a major source of global methane emissions, and methanogenic archaea could be detected in all spatial compartments of field-grown rice. The depth and scale of this study were used to build coabundance networks that revealed potential microbial consortia, some of which were involved in methane cycling. Dynamic changes observed during microbiome acquisition, as well as steady-state compositions of spatial compartments, support a multistep model for root microbiome assembly from soil wherein the rhizoplane plays a selective gating role. Similarities in the distribution of phyla in the root microbiomes of rice and other plants suggest that conclusions derived from this study might be generally applicable to land plants.Land plants grow in soil, placing them in direct proximity to a high abundance of microbial diversity (1). Plants and microbes have both adapted to use their close association for their mutual benefit. Critical nutrients are converted to more usable forms by microbes before assimilation by plants (2–4). In turn, bacteria in the rhizosphere receive carbon metabolites from the plant through root exudates (5). Beneficial soil microbes also contribute to pathogen resistance, water retention, and synthesis of growth-promoting hormones (6–8).Recent studies have used high-throughput sequencing to provide new insights into the bacterial composition and organization of different plant microbiomes, including Arabidopsis, Populus, and maize (9–14). Detailed characterization of the core root microbiome of Arabidopsis (9–11) showed that the dominant phyla inside the root (the endosphere) are much less diverse than the phyla in the soil around the root (the rhizosphere), and a potential core root microbiome could be identified. In Arabidopsis, the endophytic microbiome exhibits some genotype-dependent variation within the species and an increased variation when other related species are examined (9–11). A recent study in maize examined microbiome variation across many different inbred lines at different sites and found a large variation arising from geographical location between three different states in the United States and a relatively smaller dependence on the genotype (12). Although the microbiomes examined in the maize study consisted of combined rhizospheric and endospheric microbes (12), a study in poplar found that the variation between locations in two different states affected both rhizospheric and endospheric microbes (14).These studies have opened the way toward a new understanding of the composition and structure of plant microbiomes and the factors that affect them. However, this understanding is still at the initial stages, and several key questions are as yet unanswered. One such question regards the mechanism of microbiome acquisition and assembly in plants. Unlike animals, where the gut microbiome is assembled internally and is transmissible through birth (15, 16), the root microbiome is predominantly assembled from the external microbes in the soil. Based on the composition of the endospheric and rhizopheric microbiomes, it has been proposed that plants might assemble their microbiomes in two steps, with the first step involving a general recruitment to the vicinity of the root and a second step for entry inside the root that involves species-specific genetic factors (7). Although this is a plausible hypothesis, direct support for this model through detailed dynamic studies has not yet been provided. Additionally, the role of the root surface or rhizoplane, which forms the critical interface between plants and soil, remains poorly understood, and the microbial composition of the rhizoplane in relation to those of the rhizosphere and endosphere is unknown.To address some of these questions, we have undertaken an exhaustive characterization of the root-associated microbiome of rice. Rice is a major crop plant and a staple food for half of the world’s population. Metagenomic and proteomic approaches have been used to identify different microbial genes present in the rice microbiome (17, 18), but an extensive characterization of microbiome composition and variation has not been performed. Rice cultivation also contributes to global methane, accounting for an estimated 10–20% of anthropogenic emissions, due to the growth of methanogenic archaea in the vicinity of rice roots (19). Here we have used deep sequencing of microbial 16S rRNA genes to detect over 250,000 operational taxonomic units (OTUs), with a structural resolution of three distinct compartments (rhizosphere, rhizoplane, and endosphere) and extending over multiple factors contributing to variation, both under controlled greenhouse conditions as well as different field environments. The large datasets from the different conditions sampled in this study were used for identification of putative microbial consortia involved in processes such as methane cycling. Through dynamic studies of the microbiome composition, we provide insights into the process of root microbiome assembly.     

Human symbionts inject and neutralize antibacterial toxins to persist in the gut

The human gut microbiome is a dynamic and densely populated microbial community that can provide important benefits to its host. Cooperation and competition for nutrients among its constituents only partially explain community composition and interpersonal variation. Notably, certain human-associated Bacteroidetes—one of two major phyla in the gut—also encode machinery for contact-dependent interbacterial antagonism, but its impact within gut microbial communities remains unknown. Here we report that prominent human gut symbionts persist in the gut through continuous attack on their immediate neighbors. Our analysis of just one of the hundreds of species in these communities reveals 12 candidate antibacterial effector loci that can exist in 32 combinations. Through the use of secretome studies, in vitro bacterial interaction assays and multiple mouse models, we uncover strain-specific effector/immunity repertoires that can predict interbacterial interactions in vitro and in vivo, and find that some of these strains avoid contact-dependent killing by accumulating immunity genes to effectors that they do not encode. Effector transmission rates in live animals can exceed 1 billion events per minute per gram of colonic contents, and multiphylum communities of human gut commensals can partially protect sensitive strains from these attacks. Together, these results suggest that gut microbes can determine their interactions through direct contact. An understanding of the strategies human gut symbionts have evolved to target other members of this community may provide new approaches for microbiome manipulation.Interpersonal variation in gut microbial community composition, even at the species or strain level, can determine the contribution of these communities to cancer risk, drug metabolism, caloric extraction from diet, infectious disease resistance, and other responses (1–5). However, the rules that determine community membership, especially at the species or strain level, are largely undefined. The gut environment is characterized by constant peristalsis and extensive niche heterogeneity, and factors previously implicated in shaping these communities (metabolites, vitamins, dietary polysaccharides, host IgA, bacteriocins) are freely diffusible (6–8). In this context, the recent identification of genes encoding type VI secretion systems (T6SSs) in the genomes of many prominent human gut symbionts was unexpected because the ability of these dynamic machines to inject toxic effectors into adjacent cells is strictly dependent on direct cell-to-cell contact (9–12).The T6SSs of Bacteroidetes share many subunits with those of Proteobacteria; these include the Hcp and TssB–TssC proteins, which interact and assemble into a contractile bacteriophage tail-like structure that is required for effector translocation from donor to recipient cells (9, 10). Bacteria with T6SSs lack a means for self-/non–self-discrimination; thus, sister cells inject one another with effectors. To nullify the antibacterial properties of these toxins, T6SS⁺ strains produce immunity proteins that directly bind cognate effectors. Despite our growing understanding of the mechanism and activity of T6S in vitro, little is known about the ecological role of this pathway in natural environments where direct encounters between microorganisms occur.Here we report that the human gut symbiont Bacteroides fragilis NCTC 9343 (B. fragilis^N) targets other members of the microbiome in a species- and strain-specific manner in the mammalian gut. We identify strain-specific effector/immunity (E/I) repertoires and show that the presence or absence of these genes can accurately predict interstrain dynamics in the gut. Furthermore, we combine microbial genetics, mathematical modeling, and gnotobiotic studies to determine the frequency of T6S-mediated events in live animals. Together, these results define a significant role for contact-mediated bacterial antagonism between human gut symbionts.     

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest

The phyllosphere—the aerial surfaces of plants, including leaves—is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density–growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant–microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function.The phyllosphere—the aerial surfaces of plants—is an important and ubiquitous habitat for bacteria (1). It is estimated that on a global scale, the phyllosphere spans more than 10⁸ km² and is home to up to 10²⁶ bacterial cells (2). Bacteria are also important to their plant hosts. Leaf-associated bacteria represent a widespread and ancient symbiosis (3, 4) that can influence host growth and function in many ways, including the production of growth-promoting nutrients and hormones (5, 6) and protection of hosts against pathogen infection (7, 8). Phyllosphere bacteria have the potential to influence plant biogeography and ecosystem function through their influence on plant performance under different environmental conditions (9–11), but the drivers of variation in leaf-associated bacterial biodiversity among host plants are not well understood.The ability to quantify microbial community structure in depth with environmental sequencing technologies has led to an increasing focus not only on the ecology of individual microbial taxa but on the entire genomic content of communities of microbes in different habitats, or “microbiomes” (12). Numerous studies of host-associated microbiomes have shown that microbial biodiversity is a trait (13) that forms part of the extended phenotype of the host organism (4, 14, 15) with important effects on the health and fitness (16–18) and evolution (19–21) of the host. Because of the importance of the microbiome for host fitness and function, there is a growing desire to model and manage host–microbiome interactions (22, 23), and understanding the drivers of host-associated microbial community assembly has thus become a cornerstone of microbiome research (24).In animals, the assembly of host-associated microbiomes is known to be driven by ecologically important host attributes, such as diet, that covary with host evolutionary history (20, 25, 26). A similar understanding of the drivers of plant microbiome assembly is lacking. Most of our knowledge of plant–bacterial associations on leaves has been based on studies of individual bacterial strains and individual host species. Different plant species possess characteristic bacterial phyllosphere communities (27, 28), and there are several examples of variation in bacterial biodiversity on leaves among plant genotypes (29–31) as well as among species and higher taxonomic ranks (32). Although these patterns are presumably due to phylogenetic variation in ecologically important plant functional traits (33) among host populations and species, the influence of host functional traits on variation in phyllosphere community structure across host species has not been directly quantified. As a result, we have very little understanding of the potential of plant–microbe interaction networks to influence the distribution and functional biogeography of their hosts at large scales in the face of global change (34).A first step toward integrating phyllosphere microbial communities into the study of plant biogeography will require establishing correlations between microbial community structure on leaves and the functional traits of plant hosts. To address this goal, we used high-throughput sequencing to characterize the structure of the bacterial phyllosphere microbiome on the leaves of multiple host tree species in a diverse neotropical forest in Panama. We combined phyllosphere microbiome data with a rich dataset on the attributes of plant hosts, including functional traits and evolutionary relationships, to (i) quantify the magnitude of leaf-associated bacterial biodiversity in a diverse natural forest community, (ii) identify the host plant attributes that influence microbiome community assembly on leaves, and (iii) understand relationships between bacterial biodiversity and suites of host plant traits and functions and discuss their implications for our understanding of plant functional biogeography.     

Gut DNA viromes of Malawian twins discordant for severe acute malnutrition

The bacterial component of the human gut microbiota undergoes a definable program of postnatal development. Evidence is accumulating that this program is disrupted in children with severe acute malnutrition (SAM) and that their persistent gut microbiota immaturity, which is not durably repaired with current ready-to-use therapeutic food (RUTF) interventions, is causally related to disease pathogenesis. To further characterize gut microbial community development in healthy versus malnourished infants/children, we performed a time-series metagenomic study of DNA isolated from virus-like particles (VLPs) recovered from fecal samples collected during the first 30 mo of postnatal life from eight pairs of mono- and dizygotic Malawian twins concordant for healthy growth and 12 twin pairs discordant for SAM. Both members of discordant pairs were sampled just before, during, and after treatment with a peanut-based RUTF. Using Random Forests and a dataset of 17,676 viral contigs assembled from shotgun sequencing reads of VLP DNAs, we identified viruses that distinguish different stages in the assembly of the gut microbiota in the concordant healthy twin pairs. This developmental program is impaired in both members of SAM discordant pairs and not repaired with RUTF. Phage plus members of the Anelloviridae and Circoviridae families of eukaryotic viruses discriminate discordant from concordant healthy pairs. These results disclose that apparently healthy cotwins in discordant pairs have viromes associated with, although not necessarily mediators, of SAM; as such, they provide a human model for delineating normal versus perturbed postnatal acquisition and retention of the gut microbiota’s viral component in populations at risk for malnutrition.Malnutrition (undernutrition) is a leading cause of child mortality worldwide (1). Severe acute malnutrition (SAM) can manifest itself as progressive wasting (marasmus) or as a more abrupt onset syndrome characterized by generalized edema, hepatic steatosis, skin rashes and ulcerations, and anorexia (kwashiorkor). The configuration of the bacterial component of the gut microbiota of healthy infants evolves to an adult-like configuration during the first 2–3 y of life (2, 3). Normal postnatal maturation of the gut microbial community is perturbed in SAM; children with SAM living in Malawi and in Bangladesh have gut microbiota with bacterial configurations that appear younger (more immature) than the microbiota of chronologically age-matched individuals with healthy growth phenotypes (3, 4). Moreover, this immaturity is only transiently improved with current ready-to-use therapeutic food (RUTF) interventions (3, 4). These children can be viewed as having a persistent developmental abnormality—one that affects a microbial “organ” whose key functions include the biosynthesis of vitamins and the biotransformation of dietary components into products that benefit members of the gut microbial community and their host (2–5).A study of 317 twin pairs from five rural villages in southern Malawi showed that discordance for moderate acute malnutrition (MAM) and SAM was surprisingly high during the first 3 y of life (43% of pairs) and not significantly different between mono- and dizygotic pairs (concordant undernourished pairs comprised 7% of the cohort) (4). The standard of care in Malawi is to treat both cotwins in pairs discordant for marasmus or kwashiorkor with a peanut-based RUTF for several weeks until a threshold increase in weight has been achieved (both siblings in the pair are treated to avoid potential problems arising from maternal food-sharing practices that emphasize the diseased child and neglect the healthy cotwin) (4, 6). Although short-term administration of RUTF has dramatically reduced mortality, it generally does not ameliorate the long-term morbidities associated with malnutrition—stunting, neurodevelopmental abnormalities, and immune dysfunction (e.g., refs. 6–10).Transplantation of fecal samples obtained from children with kwashiorkor and their apparently healthy cotwins into separate groups of adult germ-free mice consuming a prototypic macro- and micronutrient-deficient Malawian diet resulted in transmission of discordant weight loss and metabolic and gut barrier dysfunction phenotypes to the animals. Development of these pathologic phenotypes was diet-dependent: they were not observed, or dramatically mitigated, when gnotobiotic mice harboring a kwashiorkor microbiota received a healthy diet with adequate nutrients (4, 11). Together, these findings indicate that the gut microbiota is causally related to SAM (4) but also raise the question of how discordance for SAM arises and whether the cotwin classified as “healthy” by anthropometry has an underlying perturbation in his/her gut community that reflects familial risk for development of pathology. To address these issues, we focused on the most variable component of the human gut microbial community, the DNA virome. Moreover, although surveys of DNA viruses present in the gut microbiota of healthy adults had revealed a dominance of phage, in particular of lysogenic phages (prophages) (12–15), almost nothing was known about the normal pattern of assembly of the virome and the factors that shape this aspect of postnatal microbiota development (16).     

Evolutionary limits to cooperation in microbial communities

Microbes produce many compounds that are costly to a focal cell but promote the survival and reproduction of neighboring cells. This observation has led to the suggestion that microbial strains and species will commonly cooperate by exchanging compounds. Here, we examine this idea with an ecoevolutionary model where microbes make multiple secretions, which can be exchanged among genotypes. We show that cooperation between genotypes only evolves under specific demographic regimes characterized by intermediate genetic mixing. The key constraint on cooperative exchanges is a loss of autonomy: strains become reliant on complementary genotypes that may not be reliably encountered. Moreover, the form of cooperation that we observe arises through mutual exploitation that is related to cheating and “Black Queen” evolution for a single secretion. A major corollary is that the evolution of cooperative exchanges reduces community productivity relative to an autonomous strain that makes everything it needs. This prediction finds support in recent work from synthetic communities. Overall, our work suggests that natural selection will often limit cooperative exchanges in microbial communities and that, when exchanges do occur, they can be an inefficient solution to group living.

‘Benefit-of-the-species’ arguments … provide for the reader an escape from inner conflict, exacting nothing emotionally beyond what most of us learn to accept in childhood, that most forms of life exploit and prey on one another.

Hamilton, 1975 (1)

Microbes typically live in dense communities containing many strains and species. These genetically diverse societies are widespread and central to how microbes affect us, including examples such as the gut microbiome, polymicrobial infections, and communities vital to bioremediation and nutrient cycling (2, 3). In these collectives, ecological interactions are thought to be both common and strong given that cell density is typically high and that microbes possess many phenotypes that influence the reproduction and survival of surrounding cells (4, 5). Such social traits include many secretions, such as extracellular enzymes and scavenging molecules (4–6), and other beneficial “leaky” traits, such as detoxification agents (7) or amino acids (8, 9).A central explanation for cooperative phenotypes in microbes is that they function to help cells of the same genotype (10, 11), which is backed up by a growing body of theory and experiments (12–18). However, it is also clear that, in nature, microbes commonly interact with many different genotypes (both different strains and species) in complex ecological networks (19–21). Do these different microbial genotypes cooperate with one another? Understanding this question is central to building models of microbial communities and how they will respond to both environmental and anthropogenic perturbations (22).Studies involving genetically engineered (8, 9, 23, 24) and/or artificially selected communities (23, 25, 26) emphasize how easily cooperation between genotypes can be achieved in the laboratory. Additionally, there are a growing number of suggestions that cooperation should commonly evolve between microbial strains and species (27–30). This view contrasts with empirical surveys of natural bacterial communities, which suggest that competitive interactions predominate over cooperative interactions (31). However, it has also been suggested that cooperation between different genotypes may explain the unculturability of many species in the laboratory when in monoculture (32–34). If correct, studies with culturable species could underestimate cooperativity in microbial communities.The potential for cooperation between different microbial genotypes then remains unclear. Indeed, we even lack clear predictions of what to expect. There is a need for general theory on cooperation between microbial genotypes. One microbial interaction that has been explored theoretically is syntrophy, where one species produces a toxic waste product that another species consumes (35–38). Syntrophy is likely to be ecologically important and under some conditions (36), can benefit both species. However, syntrophic species need not pay energetic costs to interact: one species is producing waste, and the other species is feeding. Such byproduct cooperation can, therefore, readily evolve but is fundamentally different to the exchange of costly secretions (39, 40). Other models have analyzed when costly cooperation between species is expected in microbes and other organisms (35, 39, 41). However, these models assume that there is no opportunity for one partner to express the beneficial trait of the other. Although this constraint will sometimes occur, there is considerable functional overlap in the cooperative traits of microbial species (7). In addition, the potential for horizontal gene transfer in microbes means that there is a broad scope for a focal strain to pick up the phenotypes of co-occurring strains and species (42–44).Here, we examine the potential for microbial cooperation between different strains and species. We base our work on the well-established models of within-genotype microbial cooperation for a single public good (12, 18, 45–47) so that the relationship to previous work is clear (SI Materials and Methods). We add one key feature to these models: we allow cells to invest in multiple distinct cooperative secretions, such that there is the potential for different genotypes to exchange secretions with one another. Our analysis shows that the degree of genetic mixing defines the potential for cooperation both within and between genotypes. Low mixing favors genotypes that produce all secretions, whereas high mixing favors genotypes that do not produce any at all. Only for intermediate levels of genetic mixing do we find between-genotype cooperation, where strains produce a subset of secretions and rely on other genotypes for the complementary traits. Moreover, the form of cooperation that emerges is inefficient and results in a loss of productivity relative to one genotype making all secretions. Natural selection limits both the occurrence and effectiveness of cooperation within microbial communities.     

Global dispersion and local diversification of the methane seep microbiome

Methane seeps are widespread seafloor ecosystems shaped by the emission of gas from seabed reservoirs. The microorganisms inhabiting methane seeps transform the chemical energy in methane to products that sustain rich benthic communities around the gas leaks. Despite the biogeochemical relevance of microbial methane removal at seeps, the global diversity and dispersion of seep microbiota remain unknown. Here we determined the microbial diversity and community structure of 23 globally distributed methane seeps and compared these to the microbial communities of 54 other seafloor ecosystems, including sulfate–methane transition zones, hydrothermal vents, coastal sediments, and deep-sea surface and subsurface sediments. We found that methane seep communities show moderate levels of microbial richness compared with other seafloor ecosystems and harbor distinct bacterial and archaeal taxa with cosmopolitan distribution and key biogeochemical functions. The high relative sequence abundance of ANME (anaerobic methanotrophic archaea), as well as aerobic Methylococcales, sulfate-reducing Desulfobacterales, and sulfide-oxidizing Thiotrichales, matches the most favorable microbial metabolisms at methane seeps in terms of substrate supply and distinguishes the seep microbiome from other seafloor microbiomes. The key functional taxa varied in relative sequence abundance between different seeps due to the environmental factors, sediment depth and seafloor temperature. The degree of endemism of the methane seep microbiome suggests a high local diversification in these heterogeneous but long-lived ecosystems. Our results indicate that the seep microbiome is structured according to metacommunity processes and that few cosmopolitan microbial taxa mediate the bulk of methane oxidation, with global relevance to methane emission in the ocean.A microbiome is defined as the microbial community and its genomic diversity associated with a particular ecosystem or habitat, such as soil (1) or the human gut (2). A key question in the study of microbiomes concerns the identification of assembly rules that govern microbial community structure and community function (3). Sampling efforts on local to global scales have been used to determine the key drivers of microbial assembly, which include processes such as dispersal, ecological drift, environmental selection, and diversification (3, 4). Major processes shaping the microbial diversity landscape involve environmental selection of organisms according to their traits, niche preferences, biological interactions, and coevolution with hosts (5, 6). In turn, recent findings suggest that fluctuations of key microbial taxa reflect the dynamics of important biogeochemical processes (7).Insights into environmental microbiomes have tremendously improved with the use of next-generation sequencing methods and global databases, which have advanced microbial ecology from the identification of rare members of microbial communities (8) to global microbial distribution patterns (9, 10). Benthic (seafloor-hosted) microbial communities of the ocean are very distinct from pelagic (seawater-hosted) communities (9) and are impacted by water depth (11, 12), sediment depth (13, 14), and by energy availability in the form of deposited organic matter (12, 15, 16). Marine sediments are known to host communities as diverse as those found in soils, with pronounced community turnover on small (decimeter to kilometer), intermediate (hundreds of kilometers), and large (thousands of kilometers) spatial scales (17, 18).Cold seeps are distinct seafloor ecosystems that are defined by the upward advection of methane and other hydrocarbons from the subsurface seabed to the seafloor (19). Gas-emitting methane seeps are found scattered on continental margins worldwide and are separated by large expanses of energy-limited, aerobic deep-sea seafloor where the benthic communities depend on sparse detritus flux. These seeps can be regarded as patches of a certain habitat type, offering niches that differ strongly from the surrounding seafloor (14, 20, 21). Typically, methane seep sediments are highly reduced, and oxygen availability is limited to a few millimeters to centimeters of the sediment surface. Below that thin oxic zone, methane is consumed by microbial consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB) mediating the anaerobic oxidation of methane (AOM) coupled to sulfate reduction (22). This microbial conversion of inorganic energy sources fuels communities of microorganisms and marine invertebrates and thus generates hotspots of biomass and diversity in the deep sea (23). Together, micro- and macroorganisms at methane seeps and sulfate methane transition zones (SMTZ) consume 75% of the methane (0.06 Gt of carbon per year) that reaches the surface seafloor from subsurface zones (19). Hence, they provide a globally relevant ecosystem function by controlling the emission of the potential greenhouse gas methane from the ocean.At large scales, however, it is unclear which seep microorganisms are important for the removal of methane and which mechanisms govern their community assembly. Defining the methane seep microbiome is needed to identify the microbial key players responsible for these important biogeochemical functions. In this study, we compared the archaeal and bacterial diversity of 23 globally distributed methane seeps to that of 54 globally distributed sites from other seafloor ecosystems, including deep SMTZ, hydrothermal vents, coastal sediments, and deep-sea surface and subsurface sediments. We tested (i) whether methane seeps are island-like habitats that are similar to each other but distinct from their surroundings concerning community richness, evenness, similarity, and composition; (ii) if a core set of associated bacteria and archaea dominates seeps globally; and (iii) whether their assembly patterns follow the metacommunity concept of globally dispersed and locally diversified types (24).     

Rapid changes in the gut microbiome during human evolution

Humans are ecosystems containing trillions of microorganisms, but the evolutionary history of this microbiome is obscured by a lack of knowledge about microbiomes of African apes. We sequenced the gut communities of hundreds of chimpanzees, bonobos, and gorillas and developed a phylogenetic approach to reconstruct how present-day human microbiomes have diverged from those of ancestral populations. Compositional change in the microbiome was slow and clock-like during African ape diversification, but human microbiomes have deviated from the ancestral state at an accelerated rate. Relative to the microbiomes of wild apes, human microbiomes have lost ancestral microbial diversity while becoming specialized for animal-based diets. Individual wild apes cultivate more phyla, classes, orders, families, genera, and species of bacteria than do individual humans across a range of societies. These results indicate that humanity has experienced a depletion of the gut flora since diverging from Pan.The human microbiome is shaped by host genetics, environment, and lifestyle (1–3); thus, humanity''s unique evolutionary and cultural histories must have altered our associations with microorganisms (4). Despite intensive investigation of the microbiomes of humans spanning a range of geographic locations and cultures (5–7), how the composition of the microbiome has changed since humans diverged from other species, and since human populations diverged from one another, remains unclear, owing to a lack of knowledge about the microbiomes of ancestral hominid populations.Understanding how the composition of the human microbiome has changed over evolutionary time requires the inclusion of the microbiomes of phylogenetic outgroups (i.e., the African apes) into analyses of human microbiomes. Previous comparisons of the gut microbiomes of humans and the African apes have been restricted to just a few individuals per host species (8), precluding detection of the precise compositional differences that distinguish the microbiomes of the host species. Comparing the microbiomes of populations of chimpanzees, bonobos, gorillas, and humans while considering the phylogenetic relatedness among the hosts can reveal how the composition of the microbiome has changed since the host species diversified.Here we used a phylogenetic approach to identify the shifts in the composition of the microbiome that occurred along the lineages leading to the extant species of Homo and Pan. This analysis shows that humans across a range of cultures and geographies harbor microbiomes that are disproportionately divergent from those within wild apes. In particular, among the living hominid species, humans harbor uncharacteristically low levels of microbial diversity within their gut microbiomes.     

Polymers in the gut compress the colonic mucus hydrogel

Colonic mucus is a key biological hydrogel that protects the gut from infection and physical damage and mediates host–microbe interactions and drug delivery. However, little is known about how its structure is influenced by materials it comes into contact with regularly. For example, the gut abounds in polymers such as dietary fibers or administered therapeutics, yet whether such polymers interact with the mucus hydrogel, and if so, how, remains unclear. Although several biological processes have been identified as potential regulators of mucus structure, the polymeric composition of the gut environment has been ignored. Here, we demonstrate that gut polymers do in fact regulate mucus hydrogel structure, and that polymer–mucus interactions can be described using a thermodynamic model based on Flory–Huggins solution theory. We found that both dietary and therapeutic polymers dramatically compressed murine colonic mucus ex vivo and in vivo. This behavior depended strongly on both polymer concentration and molecular weight, in agreement with the predictions of our thermodynamic model. Moreover, exposure to polymer-rich luminal fluid from germ-free mice strongly compressed the mucus hydrogel, whereas exposure to luminal fluid from specific-pathogen-free mice—whose microbiota degrade gut polymers—did not; this suggests that gut microbes modulate mucus structure by degrading polymers. These findings highlight the role of mucus as a responsive biomaterial, and reveal a mechanism of mucus restructuring that must be integrated into the design and interpretation of studies involving therapeutic polymers, dietary fibers, and fiber-degrading gut microbes.Biological hydrogels (including mucus, blood clots, and the extracellular matrix) provide critical functions, yet little is known about how their structure is influenced by materials they come into contact with regularly. For example, the environments of many hydrogels abound in polymers, such as dietary fibers (1, 2) or administered therapeutics (3–5) in the gut and soluble glycoproteins in tissues. Whether such polymers interact with these hydrogels, and if so, how, remains unclear. An important example is the case of colonic mucus, which protects the gut from infection and physical damage (6–8), mediates drug delivery (9), and mediates host–microbe interactions (10) in a structure-dependent manner; for example, a “tighter” mesh could impede the infiltration of microorganisms from the intestinal lumen (6, 11–13). Mucus restructuring is typically attributed solely to changes in secretion (14–16), or to the activity of specific enzymes (8, 17), detergents (18), or dextran sulfate sodium-induced inflammation (19). However, the physicochemical properties of the gut environment itself—particularly its polymeric composition—have not been considered as a potential regulator of mucus structure. We therefore sought to characterize the structure of the colonic mucus hydrogel in the absence and in the presence of polymers.     

Intestinal permeability,gut-bacterial dysbiosis,and behavioral markers of alcohol-dependence severity

Alcohol dependence has traditionally been considered a brain disorder. Alteration in the composition of the gut microbiota has recently been shown to be present in psychiatric disorders, which suggests the possibility of gut-to-brain interactions in the development of alcohol dependence. The aim of the present study was to explore whether changes in gut permeability are linked to gut-microbiota composition and activity in alcohol-dependent subjects. We also investigated whether gut dysfunction is associated with the psychological symptoms of alcohol dependence. Finally, we tested the reversibility of the biological and behavioral parameters after a short-term detoxification program. We found that some, but not all, alcohol-dependent subjects developed gut leakiness, which was associated with higher scores of depression, anxiety, and alcohol craving after 3 wk of abstinence, which may be important psychological factors of relapse. Moreover, subjects with increased gut permeability also had altered composition and activity of the gut microbiota. These results suggest the existence of a gut–brain axis in alcohol dependence, which implicates the gut microbiota as an actor in the gut barrier and in behavioral disorders. Thus, the gut microbiota seems to be a previously unidentified target in the management of alcohol dependence.Alcohol consumption is the world’s third largest risk factor for disease and disability and accounts for 5.9% of all deaths worldwide (1). Although alcohol exerts large deleterious effects on health, studies to date on the pathophysiology of alcohol dependence have mainly focused on the influence of alcohol consumption on neuronal functions in the brain (2). A limited number of studies have, however, suggested that gut functions might also be altered by chronic alcohol consumption (3, 4). Accordingly, we and others have shown that actively drinking alcohol-dependent (AD) subjects exhibited increased intestinal permeability (IP) and increased plasma levels of gut-derived bacterial products such as lipopolysaccharides and peptidoglycans (5–8). These bacterial products activate specific inflammatory pathways that partially recover after a 3-wk period of alcohol abstinence (5, 6). These recent observations indirectly suggest the possibility that the composition of gut microbiota could be altered in AD subjects and related to behavioral symptoms.The human gut microbiota consists of a complex community exceeding 100 trillion microorganisms (9) whose collective genome—the microbiome—encodes 100 times more genes than the human genome (10). It is now widely accepted that the gut microbiota should be considered an “exteriorized” organ placed within the body, which provides important physiological functions and is indispensable for human life (10–12). However, the microbial composition or activity of the gut can be modified by diet, antibiotic use, host genetics, and other environmental factors (13). Data suggest that an imbalance of the intestinal microbiota, known as dysbiosis, may contribute to a variety of somatic diseases such as obesity (14), type 2 diabetes (15), inflammatory bowel diseases (16, 17), and allergy (18).Recent studies suggest that the gut bacteria also influence brain functions and behavior and may therefore play a role in the development of psychiatric disorders (19). Indeed, in experimental studies, researchers observed that germfree mice displayed reduced anxiety-like behavior compared with mice with normal gut microbiota, demonstrating evidence of gut-to-brain interactions (20, 21). Further studies brought forward evidence that the pathways underlying the gut–brain axis are multiple and highly complex, involving brain biochemistry, the vagus nerve, proinflammatory cytokines, and tryptophan metabolism (22). Furthermore, inflammation and tryptophan/kynurenine pathways have been related to the development of depression-like behavior (23–26). In addition, gut bacteria produce neurotransmitters (serotonin, GABA, dopamine, acetylcholine), and bacterial fermentation of dietary fiber induces the release of short-chain fatty acids, which are metabolites with potential neuroactive properties (22). Recent evidence also suggests that Bacteroides fragilis may prevent autism spectrum disorder in a mouse model (27) and that administration of probiotic Bifidobacterium infantis may have antidepressant properties in rats through changes in the tryptophan/kynurenine pathway (26). Although several animal studies support a relation between the gut microbiota and behavior, major questions remain regarding this relation in human health.Depression and anxiety frequently develop in actively drinking AD subjects and play an important role in the negative reinforcement of drinking tendency (28). These factors are strongly related to the urge to drink, hereafter referred to as alcohol craving (29, 30), an important predictor of relapse after detoxification (31). The possibility that these psychological symptoms of addiction are related to a dysbiosis has so far never been investigated. The aim of the present study was to determine whether gut permeability could be associated to the severity of psychological symptoms (depression, anxiety, and craving) developed by human AD subjects. Then, we assessed the composition and activity of the gut microbiota and tested whether they are related to gut permeability. Finally, we analyzed whether alterations in gut permeability, microbiota composition, and metabolome are reversible after 3 wk of alcohol withdrawal, which is known to induce partial recovery of psychiatric symptoms (32).     

Gut bacteria mediate aggregation in the German cockroach

Aggregation of the German cockroach, Blattella germanica, is regulated by fecal aggregation agents (pheromones), including volatile carboxylic acids (VCAs). We demonstrate that the gut microbial community contributes to production of these semiochemicals. Chemical analysis of the fecal extract of B. germanica revealed 40 VCAs. Feces from axenic cockroaches (no microorganisms in the alimentary tract) lacked 12 major fecal VCAs, and 24 of the remaining compounds were represented at extremely low amounts. Olfactory and aggregation bioassays demonstrated that nymphs strongly preferred the extract of control feces over the fecal extract of axenic cockroaches. Additionally, nymphs preferred a synthetic blend of 6 fecal VCAs over a solvent control or a previously identified VCA blend. To test whether gut bacteria contribute to the production of fecal aggregation agents, fecal aerobic bacteria were cultured, isolated, and identified. Inoculation of axenic cockroaches with individual bacterial taxa significantly rescued the aggregation response to the fecal extract, and inoculation with a mix of six bacterial isolates was more effective than with single isolates. The results indicate that the commensal gut microbiota contributes to production of VCAs that act as fecal aggregation agents and that cockroaches discriminate among the complex odors that emanate from a diverse microbial community. Our results highlight the pivotal role of gut bacteria in mediating insect–insect communication. Moreover, because the gut microbial community reflects the local environment, local plasticity in fecal aggregation pheromones enables colony-specific odors and fidelity to persistent aggregation sites.Diverse microbial communities inhabit the alimentary tract and other tissues of many insect species. Their effects on the host vary, ranging from facultative provision of essential nutrients to stimulation of the immune system and exclusion of pathogenic microbes (1–6). Insect-symbiotic associations, some obligatory, are common, where hosts are nutritionally and immunologically dependent on their symbiotic microbes: Buchnera in aphids (7), nitrogen-fixing bacteria in termites (8), Blattabacterium in cockroaches (e.g., ref. 9), lactic acid bacteria in honey bees (10) and Wolbachia, which affects sex determination (11), immune function (e.g., ref. 12) and nutrition (13) in many insect species. The alimentary tract, and especially the hindgut of many (possibly all) insects, is persistently colonized by opportunistic, facultative, and commensal microbiota largely structured by exogenous (diet and local environment) and endogenous (gut environment) factors. The commensal gut microbiota can modulate various aspects of insect biology, including behavior (e.g., refs. 14–16), host–parasite and host–pathogen interactions (e.g., refs. 2 and 4), and various life history traits (1, 17).The German cockroach, Blattella germanica is a major pest of the built environment, where it can acquire and transmit pathogens, contaminate food, and produce allergenic proteins that cause human morbidity (18, 19). The German cockroach lives in aggregations (20), and contact with conspecifics accelerates nymphal development (21) and reproductive maturation in both sexes (22, 23). Younger nymphs benefit from coprophagy in aggregations (24), and gregarious behavior may also facilitate mate location, predator avoidance, thermoregulation, and prevention of water loss. Fidelity to the resting/aggregation site may also facilitate group foraging in the rapidly changing human environment. Aggregation behavior is mediated by at least two types of chemical cues: endogenous compounds produced by the insect and compounds contained in feces. Cuticular hydrocarbons facilitate aggregations (25), and salivary compounds contribute to dissolution of aggregations (26); both are examples of endogenous signals. Feces-associated compounds function as powerful attractants and arrestants in all life stages of the German cockroach (27, 28).Identification of the fecal aggregation pheromones of cockroaches has been fraught with controversy. Candidate pheromones are thought to be endogenously produced by rectal pads (29), with arrestment agents, including blattellastanoside A and B (30) and volatile carboxylic acids (VCAs) (31, 32), and attractants, including ammonia, alkyl amines, amino alcohols, alcohols (33), and VCAs (31, 32). However, the chemical profiles of aggregation-inducing agents vary greatly among reports. The structures of blattellastanosides may be an artifact of chemical isolation and fractionation (34). Some compounds are inconsistently detected in feces, and behavioral responses to them range from attraction to neutral to avoidance (32, 35). More than 150 compounds, including 57 carboxylic acids, have been identified from feces of the German cockroach (31). Because methylation decreased the aggregation response (31), a mix of VCAs was considered the likely aggregation stimuli (32).Symbiotic and commensal bacteria modulate the production of sex pheromones in grass grub beetles (36) and Drosophila (15) and the aggregation pheromone in locusts (37). We hypothesized that the fecal VCAs that mediate aggregation in the German cockroach originate from the bacterial community in the feces, and, because gut-associated bacteria are acquired from the environment, we posited that both the VCA profiles and the behavioral responses to them depend on environmental conditions. Our behavioral assays and chemical analysis revealed that the feces of axenically reared cockroaches (no microorganisms in the alimentary tract) contained many fewer VCAs and failed to elicit aggregation behavior. Inoculation with fecal aerobic bacteria rescued the aggregation activity of fecal extracts of axenic cockroaches. A synthetic blend of VCAs was an effective aggregation stimulus for German cockroaches. We propose that gut bacteria impact the production of fecal VCAs as aggregation agents and that cockroaches use fecal VCAs from commensal microbes as aggregation cues that reflect their colony odor.     

From the Cover: Why the proportion of transmission during early-stage HIV infection does not predict the long-term impact of treatment on HIV incidence

Antiretroviral therapy (ART) reduces the infectiousness of HIV-infected persons, but only after testing, linkage to care, and successful viral suppression. Thus, a large proportion of HIV transmission during a period of high infectiousness in the first few months after infection (“early transmission”) is perceived as a threat to the impact of HIV “treatment-as-prevention” strategies. We created a mathematical model of a heterosexual HIV epidemic to investigate how the proportion of early transmission affects the impact of ART on reducing HIV incidence. The model includes stages of HIV infection, flexible sexual mixing, and changes in risk behavior over the epidemic. The model was calibrated to HIV prevalence data from South Africa using a Bayesian framework. Immediately after ART was introduced, more early transmission was associated with a smaller reduction in HIV incidence rate—consistent with the concern that a large amount of early transmission reduces the impact of treatment on incidence. However, the proportion of early transmission was not strongly related to the long-term reduction in incidence. This was because more early transmission resulted in a shorter generation time, in which case lower values for the basic reproductive number (R₀) are consistent with observed epidemic growth, and R₀ was negatively correlated with long-term intervention impact. The fraction of early transmission depends on biological factors, behavioral patterns, and epidemic stage and alone does not predict long-term intervention impacts. However, early transmission may be an important determinant in the outcome of short-term trials and evaluation of programs.Recent studies have confirmed that effective antiretroviral therapy (ART) reduces the transmission of HIV among stable heterosexual couples (1–3). This finding has generated interest in understanding the population-level impact of HIV treatment on reducing the rate of new HIV infections in generalized epidemic settings (4). Research, including mathematical modeling (5–10), implementation research (11), and major randomized controlled trials (12–14), are focused on how ART provision might be expanded strategically to maximize its public health benefits (15, 16).One concern is that if a large fraction of HIV transmission occurs shortly after a person becomes infected, before the person can be diagnosed and initiated on ART, this will limit the potential impact of HIV treatment on reducing HIV incidence (9, 17, 18). Data suggest that persons are more infectious during a short period of “early infection” after becoming infected with HIV (19–22), although there is debate about the extent, duration, and determinants of elevated infectiousness (18, 23). The amount of transmission that occurs also will depend on patterns of sexual behavior and sexual networks (17, 24–27). There have been estimates for the contribution of early infection to transmission from mathematical models (7, 17, 21, 24–26) and phylogenetic analyses (28–31), but these vary widely, from 5% to above 50% (23).In this study, we use a mathematical model to quantify how the proportion of transmission that comes from persons who have been infected recently affects the impact of treatment scale-up on HIV incidence. The model is calibrated to longitudinal HIV prevalence data from South Africa using a Bayesian framework. Thus, the model accounts for not only the early epidemic growth rate highlighted in previous research (5, 9, 18), but also the heterogeneity and sexual behavior change to explain the peak and decline in HIV incidence observed in sub-Saharan African HIV epidemics (32, 33).The model calibration allows uncertainty about factors that determine the amount of early transmission, including the relative infectiousness during early infection, heterogeneity in propensity for sexual risk behavior, assortativity in sexual partner selection, reduction in risk propensity over the life course, and population-wide reductions in risk behavior in response to the epidemic (32, 33). This results in multiple combinations of parameter values that are consistent with the observed epidemic and variation in the amount of early transmission. We simulated the impact of a treatment intervention and report how the proportion of early transmission correlates with the reduction in HIV incidence from the intervention over the short- and long-term.