Mining the human gut microbiome for novel stress resistance genes

With the rapid advances in sequencing technologies in recent years, the human genome is now considered incomplete without the complementing microbiome, which outnumbers human genes by a factor of one hundred. The human microbiome, and more specifically the gut microbiome, has received considerable attention and research efforts over the past decade. Many studies have identified and quantified “who is there?,” while others have determined some of their functional capacity, or “what are they doing?” In a recent study, we identified novel salt-tolerance loci from the human gut microbiome using combined functional metagenomic and bioinformatics based approaches. Herein, we discuss the identified loci, their role in salt-tolerance and their importance in the context of the gut environment. We also consider the utility and power of functional metagenomics for mining such environments for novel genes and proteins, as well as the implications and possible applications for future research.     

Mining the human gut microbiome for novel stress resistance genes

With the rapid advances in sequencing technologies in recent years, the human genome is now considered incomplete without the complementing microbiome, which outnumbers human genes by a factor of one hundred. The human microbiome, and more specifically the gut microbiome, has received considerable attention and research efforts over the past decade. Many studies have identified and quantified “who is there?,” while others have determined some of their functional capacity, or “what are they doing?” In a recent study, we identified novel salt-tolerance loci from the human gut microbiome using combined functional metagenomic and bioinformatics based approaches. Herein, we discuss the identified loci, their role in salt-tolerance and their importance in the context of the gut environment. We also consider the utility and power of functional metagenomics for mining such environments for novel genes and proteins, as well as the implications and possible applications for future research.     

Tungsten enzymes play a role in detoxifying food and antimicrobial aldehydes in the human gut microbiome

Tungsten (W) is a metal that is generally thought to be seldom used in biology. We show here that a W-containing oxidoreductase (WOR) family is diverse and widespread in the microbial world. Surprisingly, WORs, along with the tungstate-specific transporter Tup, are abundant in the human gut microbiome, which contains 24 phylogenetically distinct WOR types. Two model gut microbes containing six types of WOR and Tup were shown to assimilate W. Two of the WORs were natively purified and found to contain W. The enzymes catalyzed the conversion of toxic aldehydes to the corresponding acid, with one WOR carrying out an electron bifurcation reaction coupling aldehyde oxidation to the simultaneous reduction of NAD⁺ and of the redox protein ferredoxin. Such aldehydes are present in cooked foods and are produced as antimicrobials by gut microbiome metabolism. This aldehyde detoxification strategy is dependent on the availability of W to the microbe. The functions of other WORs in the gut microbiome that do not oxidize aldehydes remain unknown. W is generally beyond detection (<6 parts per billion) in common foods and at picomolar concentrations in drinking water, suggesting that W availability could limit some gut microbial functions and might be an overlooked micronutrient.

The group 6 metals tungsten (W) and molybdenum (Mo) are extremely similar chemically forming isomorphic oxyanions under biologically relevant conditions in the form of tungstate (WO₄^2-) and molybdate (MoO₄^2-), respectively (1). However, while W is generally thought to be seldom used in biological systems, Mo is utilized by most life forms, including humans, who contain four Mo enzymes. Over 50 types of Mo enzymes have been characterized biochemically, and they have key roles in the global cycles of many elements, such as N, S, As, and Se. With the exception of nitrogenase, which contains an active-site [MoFe₇S₉] cluster, all Mo enzymes incorporate Mo in their active site as part of the organic pyranopterin cofactor. They are divided into three phylogenetically distinct Mo-containing families, DMSO reductase (DMSOR), xanthine oxidase (XO), and sulfite oxidase (SO), which have different active-site configurations and pyranopterin cofactor modifications (1). However, while W is typically regarded as a Mo antagonist (2), it has been known for decades that a very limited number of members of the DMSOR family, including some formate and formyl methanofuran dehydrogenases, are able to incorporate W, and the resulting W enzymes are functional (3–5).A fourth pyranopterin-containing enzyme family that utilizes only W but not Mo is known that was originally discovered in a thermophilic bacterium and has been extensively characterized in so-called hyperthermophilic Archaea (4, 6). These Archaea grow optimally near 100 °C in volcanic vents, and some of them contain five members of this tungsten oxidoreductase or WOR family, all of which oxidize various types of aldehyde (previously known as the aldehyde oxidoreductase or AOR family) (7, 8). The WOR family is phylogenetically unrelated to the three major families of Mo enzyme (1), although the W in the WOR is coordinated to the same type of pyranopterin-based cofactor that binds Mo in the ubiquitous Mo enzymes (9). So far, all purified members of the WOR family only contain W and not Mo, with the exception of the WOR family member YdhV very recently characterized from Escherichia coli. Of unknown function, this enzyme when artificially overexpressed in E. coli can contain either W or Mo, depending on the growth conditions (10). Two phylogenetically distinct tungstate transporters, TupABC and WtpABC, are typically found in microorganisms that contain WOR family enzymes or W-utilizing DMSOR family enzymes, and these have a much higher affinity for tungstate compared to molybdate (11, 12). The molybdate transporter, ModABC, which is much more ubiquitous than either the Tup or Wtp systems in the microbial world, typically has comparable binding affinities for molybdate and tungstate, even though in most natural environments, Mo is usually at higher concentrations by at least an order of magnitude (13). Hence, E. coli, which has several Mo enzymes in addition to the WOR family member YdhV, contains ModABC but not TupABC or WtpABC.Recently, two additional WOR family enzymes were characterized from a cellulose-degrading thermophilic bacterium (14), in which the WOR (termed GOR) oxidizes glyceraldehyde-3-phosphate (GAP) in glycolysis, and from an aromatic-degrading mesophilic bacterium (15), in which the WOR (benzoyl-CoA reductase [BCR]) reduces an aromatic ring. BCR is the first example of a nonaldehyde reaction catalyzed by a WOR family enzyme. These recent discoveries suggest that the WOR family may be more widespread and diverse in the microbial world than was originally thought. As shown in Fig. 1A, this is indeed the case. We analyzed more than 4,000 WOR family members (14) and found that they can be phylogenetically grouped into 92 clades, the vast majority of which are completely uncharacterized. Only four of the 92 clades contain a WOR whose physiological substrate is known [termed AOR (16, 17), GAPOR (18), GOR (14), and BCR (15)]. A W-containing WOR family member has also been purified from each of three other clades, but their metabolic roles have not been elucidated (SI Appendix, Table S1). Nothing is known about the other 85 WOR family clades. Even more surprising, as shown in Fig. 1A, the WOR family is well represented in microbes that inhabit the human gut.Open in a separate windowFig. 1.Phylogenetic tree of tungsten-containing WOR family enzymes and proposed physiological roles of representative members of key WOR clades in aldehyde detoxification. (A) The phylogenetic tree is comprised of 4,063 member proteins (Dataset S1) and systematically classified into 92 clades. The clades and single leaf nodes are numbered from 1 to 92, starting at the root and proceeding clockwise. Only five clade numbers are shown at the tip of clades for simplicity. Four clades (20, 22, 62, and 87) have a WOR whose physiological substrate and function are known, and these are indicated with an asterisk. The 24 leaves or clades shown in red contain one or more proteins with BLASTP E-values of 0 and an identity >45% to a UHGP-95 protein. Actual numbers of UHGP-95 proteins in each clade are given in SI Appendix, Table S1. The outer triangles (green) indicate the clades that contain the five WORs in A. mobile (clades 48 and 52 currently have no UHGP-95 members). The clade shapes indicate the estimated branch lengths of the protein members within the clade (long clades for long branch lengths). The phylogenetic tree and the associated bootstrap values are found in Dataset S2. (B) Proposed roles of bifurcating (BF-WOR) and nonbifurcating (WOR) types of tungsten-containing oxidoreductase in the detoxification of gut aldehydes.Our understanding of how microbes impact human health has been revolutionized over the past decade with the development of the NIH Human Genome Project (HMP) and related global projects (19–23). The composition and diversity of the human microbiome is affected by age, geography, and lifestyle (24), and while gut microbes aid in digestion and provide us with a variety of nutrients, they also dramatically impact a surprisingly extensive range of human diseases and conditions (25–29). Our gut is dominated by members of the phyla Firmicutes and Bacteroidetes (19), while less abundant phyla include Proteobacteria and Synergistetes; however, in virtually all cases, the metabolisms of gut representatives and how they influence the human condition are poorly understood. At first glance, the idea that W may play a role in human gut microbes would seem far-fetched, as most W-related human studies focus on the toxic effects of W (30). Herein, we investigated whether WOR-containing microbes representing the Firmicutes and Synergistetes in the human gut microbiome do indeed take up W and incorporate it into their WOR enzymes.     

Life-long dynamics of the swine gut microbiome and their implications in probiotics development and food safety

ABSTRACT

The swine gut microbiome has received remarkable attention in recent years given that pigs serve not only as important sources for animal-derived food but also as excellent biomedical models for human health. However, despite recent advances in the understanding of the swine gut microbiome, many important biological and ecological questions are still largely unanswered. In a recent study, we characterized the life-long dynamics of the swine gut microbiome from birth to market. We showed distinct shifts in gut microbiome structure along different growth stages mainly driven by diet. Here, we summarize these discoveries and provide additional data related to the core swine gut microbiome, probiotics development in the swine industry, and foodborne pathogens in the pork supply chain.     

Antibiotics,gut microbiome and obesity

Antibiotics have been hailed by many as “miracle drugs” that have been effectively treating infectious diseases for over a century, leading to a marked reduction in morbidity and mortality. However, with the increasing use of antibiotics, we are now faced not only with the increasing threat of antibiotic resistance, but also with a rising concern about potential long‐term effects of antibiotics on human health, including the development of obesity. The obesity pandemic continues to increase, a problem that affects both adults and children alike. Disruptions to the gut microbiome have been linked to a multitude of adverse conditions, including obesity, type 2 diabetes, inflammatory bowel diseases, anxiety, autism, allergies, and autoimmune diseases. This review focuses on the association between antibiotics and obesity, and the role of the gut microbiome. There is strong evidence supporting the role of antibiotics in the development of obesity in well‐controlled animal models. However, evidence for this link in humans is still inconclusive, and we need further well‐designed clinical trials to clarify this association.     

Understanding the role of the gut ecosystem in diabetes mellitus

Diabetes mellitus is a type of metabolic disorder whereby patients are unable to regulate glycemia. It is currently a worldwide public health issue, and is a burden to society because of its disabling and common complications. Diabetes is multifactorial, and also induces the onset of other diseases. In the present report, we review the labyrinth encompassing the gut microbiota and gut microbiota‐derived metabolites in type 1 diabetes and type 2 diabetes pathogenesis. There have been exceptional improvements in deoxyribonucleic acid sequencing and mass spectrometry technologies throughout these past years, and these have allowed the comprehensive collection of information on our unique gut ecosystem. We would like to advocate incorporating metagenome and metabolome information for a comprehensive perspective of the complex interrelationships between the gut environment, host metabolism and diabetes pathogenesis. We hope that with this improved understanding we would be able to provide exciting novel therapeutic approaches to engineer an ideal gut ecosystem for optimal health.     

Associations between the gut microbiome and metabolic,inflammatory, and appetitive effects of sleeve gastrectomy

The complex and multifactorial etiology of obesity creates challenges for its effective long-term management. Increasingly, the gut microbiome is reported to play a key role in the maintenance of host health and wellbeing, with its dysregulation associated with chronic diseases such as obesity. The gut microbiome is hypothesized to contribute to obesity development and pathogenesis via several pathways involving food digestion, energy harvest and storage, production of metabolites influencing satiety, maintenance of gut barrier integrity, and bile acid metabolism. Moreover, the gut microbiome likely contributes to the metabolic, inflammatory, and satiety benefits and sustained weight-loss effects following bariatric procedures such as sleeve gastrectomy. While the field of gut microbiome research in relation to obesity and sleeve gastrectomy outcomes is largely in its infancy, the gut microbiome nonetheless holds great potential for understanding some of the mechanisms behind sleeve gastrectomy outcomes as well as for optimizing post-surgery benefits. This review will explore the current literature within the field as well as discuss the current limitations, including the small sample size, variability in methodological approaches, and lack of associative data, which need to be addressed in future studies.     

Obesity,diabetes, and the gut microbiome: an updated review

Introduction: Obesity and diabetes are two of the most prevalent health problems and leading causes of death globally. As research on the intestinal microbiome increases, so does our understanding of its intricate relationship to these diseases, although this has yet to be fully elucidated.

Areas covered: This review evaluates the role of the gut microbiome in obesity and diabetes, including the influences of internal and environmental factors. Literature searches were performed using the keywords ‘diabetes,’ ‘insulin resistance,’ ‘gut microbiome,’ ‘gut microbes,’ ‘obesity,’ and ‘weight gain.’

Expert commentary: Highlights of recent research include new findings regarding the effects of caloric restriction, which expound the importance of diet in shaping the gut microbiome, and studies reinforcing the lasting implications of antibiotic use for diabetes and obesity, particularly repeated doses in early childhood.

Mechanistically, interactions between the microbiome and the host innate immune system, mediated by TLR4-LPS signaling, have been shown to meditate the metabolic benefits of caloric restriction. Further, gut microbes haven now been shown to regulate oxygen availability via butyrate production, thus protecting against the proliferation of pathogens such as E. coli and Salmonella. However, many microbial metabolites remain unidentified and their roles in obesity and diabetes remain to be determined.     

Skin exposure to sunlight: a factor modulating the human gut microbiome composition

ABSTRACT

Background: The gut microbiome has been increasingly acknowledged as playing a pivotal role in human health. Therefore, a number of studies have focused on variables that impact its microbial structure and consequent functionality. A wide range of factors, such as diet, age, sex, life stage, behavior, ethnicity, and diseases have been considered, and strong links were set out. However, some aspects regarding the microbiome determinants are still under-explored. Discussion: Recently, Bosman et al. presented evidence that skin exposure to narrowband UVB light modulated the gut microbiome of a specific human cohort. This cohort presented an increase of biodiversity, Firmicutes and Proteobacteria, and a decrease of Bacteroidetes. Based on these findings, we revisited our data on a hunter-gatherer gut microbiome (Yanomami) and identified similarities in the gut microbiome of these two cohorts. Both presented a high abundance of Proteobacteria, which had been observed as a unique feature in the Yanomami gut microbiome, and based on Bosman et al study, could be associated with their natural sunlight exposure. Conclusion: In this commentary, we would like to point out that the human lifestyle concerning sunlight exposure should be considered as one force modulating the gut microbiome, highlighting, as proposed by Bosman et al, a novel skin-gut axis which is associated with health and disease.     

Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome

ABSTRACT

The approximately 10¹¹ viruses and microbial cells per gram of fecal matter (dry weight) in the large intestine are important to human health. The responses of three common gut bacteria species, and one opportunistic pathogen, to 117 commonly consumed foods, chemical additives, and plant extracts were tested. Many compounds, including Stevia rebaudiana and bee propolis extracts, exhibited species-specific growth inhibition by prophage induction. Overall, these results show that various foods may change the abundances of gut bacteria by modulating temperate phage and suggests a novel path for landscaping the human gut microbiome.     

高通量测序在鸟类肠道微生物中的研究进展

鸟类作为分布广泛、种群数量庞大和高度多样化的物种之一,在病原体传播中发挥了重要作用。本文综述了基于高通量测序技术的3种测序策略(16S rDNA测序、宏基因组测序和宏转录组测序)的特点及其在鸟类肠道菌群多样性、抗生素抗性基因和病原微生物发现中的应用,并对未来发展趋势进行了展望。     

Triclosan,a common antimicrobial ingredient,on gut microbiota and gut health

Triclosan (TCS) is an antimicrobial compound incorporated into more than 2,000 consumer products. This compound is frequently detected in the human body and causes ubiquitous contamination in the environment, raising concerns about its impact on human health and environmental pollution. Our recent research showed that exposure to TCS exaggerates colonic inflammation and exacerbates development of colitis-associated colon tumorigenesis, via gut microbiome-dependent mechanisms. In this review, we discussed recent research about TCS, as well as other consumer antimicrobials, on the gut microbiome and gut health.     

Characterization of the human gut microbiome during travelers' diarrhea

Alterations in the gut microbiota are correlated with ailments such as obesity, inflammatory bowel disease, and diarrhea. Up to 60% of individuals traveling from industrialized to developing countries acquire a form of secretory diarrhea known as travelers' diarrhea (TD), and enterotoxigenic Escherichia coli (ETEC) and norovirus (NoV) are the leading causative pathogens. Presumably, TD alters the gut microbiome, however the effect of TD on gut communities has not been studied. We report the first analysis of bacterial gut populations associated with TD. We examined and compared the gut microbiomes of individuals who developed TD associated with ETEC, NoV, or mixed pathogens, and TD with no pathogen identified, to healthy travelers. We observed a signature dysbiotic gut microbiome profile of high Firmicutes:Bacteroidetes ratios in the travelers who developed diarrhea, regardless of etiologic agent or presence of a pathogen. There was no significant difference in α-diversity among travelers. The bacterial composition of the microbiota of the healthy travelers was similar to the diarrheal groups, however the β-diversity of the healthy travelers was significantly different than any pathogen-associated TD group. Further comparison of the healthy traveler microbiota to those from healthy subjects who were part of the Human Microbiome Project also revealed a significantly higher Firmicutes:Bacteriodetes ratio in the healthy travelers and significantly different β-diversity. Thus, the composition of the gut microbiome in healthy, diarrhea-free travelers has characteristics of a dysbiotic gut, suggesting that these alterations could be associated with factors such as travel.     

Heritable components of the human fecal microbiome are associated with visceral fat

Obesity and its associated diseases are one of the major causes of death worldwide. The gut microbiota has been identified to have essential regulatory effects on human metabolism and obesity in particular. In a recent study we provided some insights into the link between the gut microbiota (GM) and adiposity, as well as host genetic modulation of these processes. Our results identify novel evidence of association between 6 adiposity phenotypes and faecal microbial operational taxonomic units (OTUs). Accumulation of visceral fat, a key risk factor for cardio-metabolic disease, has the strongest and most pervasive signature on the gut microbiota of the factors we examined. Furthermore, we observe that the adiposity-associated OTUs were classified as heritable and in some cases were also associated with host genetic variation at obesity-associated human candidate genes FHIT, TDRG1 and ELAVL4. This addendum confirms our previously published results in the TwinsUK cohort using a different approach to OTU clustering and multivariate analysis, and discusses further the importance of considering the GM as a complex ecosystem.     

Lactobacillus and Pediococcus ameliorate progression of non-alcoholic fatty liver disease through modulation of the gut microbiome

ABSTRACT

Targeting the gut-liver axis by modulating the gut-microbiome can be a promising therapeutic approach in nonalcoholic fatty liver disease (NAFLD). The aim of this study was to evaluate the effects of single species and a combination of Lactobacillus and Pediococcus in NAFLD mice model. Six-week male C57BL/6J mice were divided into 9 groups (n = 10/group; normal, Western diet, and 7 Western diet-strains [10⁹ CFU/g, 8 weeks]). The strains used were L. bulgaricus, L. casei, L. helveticus, P. pentosaceus KID7, and three combinations (1: L. casei+L. helveticus, 2: L. casei+L. helveticus+P. pentosaceus KID7, and 3: L. casei+L. helveticus+L. bulgaricus). Liver/Body weight ratio, serum and stool analysis, liver pathology, and metagenomics by 16S rRNA-sequencing were examined. In the liver/body ratio, L. bulgaricus (5.1 ± 0.5), L. helveticus (5.2 ± 0.4), P. pentosaceus KID7 (5.5 ± 0.5), and combination1 and 2 (4.2 ± 0.6 and 4.8 ± 0.7) showed significant reductions compared with Western (6.2 ± 0.6)(p < 0.001). In terms of cholesterol and steatosis/inflammation/NAFLD activity, all groups except for L. casei were associated with an improvement (p < .05). The elevated level of tumor necrosis factor-α/interleukin-1β (pg/ml) in Western (65.8 ± 7.9/163.8 ± 12.2) was found to be significantly reduced in L. bulgaricus (24.2 ± 1.0/58.9 ± 15.3), L. casei (35.6 ± 2.1/62.9 ± 6.0), L. helveticus (43.4 ± 3.2/53.6 ± 7.5), and P. pentosaceus KID7 (22.9 ± 3.4/59.7 ± 12.2)(p < 0.01). Cytokines were improved in the combination groups. In metagenomics, each strains revealed a different composition and elevated Firmicutes/Bacteroidetes ratio in the western (47.1) was decreased in L. bulgaricus (14.5), L. helveticus (3.0), and P. pentosaceus KID7 (13.3). L. bulgaricus, L. casei, L. helveticus, and P. pentosaceus KID7 supplementation can improve NAFLD-progression by modulating gut-microbiome and inflammatory pathway.     

Obesity and the microbiome

Obesity constitutes a significant and rapidly increasing public health challenge and is associated with significant co-morbidities and healthcare costs. Although undoubtedly multifactorial, research over the last decade has demonstrated that the microbes that colonize the human gut may contribute to the development of obesity through roles in polysaccharide breakdown, nutrient absorption, inflammatory responses and gut permeability. Studies have consistently shown that the Firmicutes to Bacteroidetes ratio, in particular, is increased in obesity and reduces with weight loss. In addition, we and others have shown that the methanogenic Archaea may also contribute to altered metabolism and weight gain in the host. However, much remains to be learned about the roles of different gut microbial populations in weight gain and obesity and the underlying mechanisms before we can begin to approach targeted treatments.