Microbial diversity of mine water at Zhong Tiaoshan copper mine, China

Microbial diversity of mine water at Zhong Tiaoshan copper mine, Shanxi province, China, was analyzed using a culture-independent 16S rRNA gene (rDNA) based on cloning approach. A total of 59 Operational Taxonomic Units (OTUs) were obtained from 226 clones from all three samples (8 OTUs from sample SX1, 25 from SX2 and 26 from SX3). 46 of them were representative OTUs and were sequenced. 93.5% of the total clones had sequences that were less than 5% difference from those in the nucleic acids database. The percentage of overlapping OTUs among samples was from 12.1% to 35.3%. Phylogenetic analysis indicated that 60.62% of the clones were affiliated with members of the Proteobacteria (alpha -3.10%, beta -24.78%, gamma -31.41%, delta -1.33%), whereas 29.20% of the clones were closely related to the Nitrospira (Leptospirillum ferrooxidans 20.80%, Leptospirillum ferriphilum 0.88% and Leptospirillum group III 7.52%, respectively). The rest clones were affiliated with the Firmicutes (2.65%) and the Bacteroidetes (7.52%). The results of Principal Component Analysis (PCA) based on the percentages of OTUs and biogeochemical data revealed that biogeochemical properties affected the diversity of microbial communities in mine water. Especially, the pH value, temperature and different concentrations of elements such as lead, zinc, sulfur, iron and copper seemed to be key factors affecting the composition and structure of microbial communities in this study.     

Occurrence of filamentous fungi in drinking water: their role on fungal-bacterial biofilm formation

Water is indispensable to life and safe and accessible supply must be available to all. The presence of microorganisms is a threat to this commitment. Biofilms are the main reservoir of microorganisms inside water distribution systems and they are extremely ecologically diverse. Filamentous fungi and bacteria can coexist inside these systems forming inter-kingdom biofilms. This review has the goal of summarizing the most relevant and recent reports on the occurrence of filamentous fungi in water distribution systems along with the current knowledge and gaps about filamentous fungal biofilm formation. Special focus is given on fungal-bacterial interactions in water biofilms.     

The role of mitochondria in cellular defense against microbial infection

Mitochondria have been long recognized for their key role in the modulation of cell death pathways. Thus, it is therefore not surprising that this organelle represents a recurrent target for pathogenic microbes, aiming to manipulate the fate of the infected host cell. More recently, mitochondria have been shown to serve as a crucial platform for innate immune signaling, as illustrated by the identification of MAVS (also known as IPS-1, VISA and Cardif), NLRX1 and STING as mitochondrial proteins. This review discusses the tight interplay between microbial infection, innate immune signaling and mitochondria.     

The microbial flora in the nasal septum area prone to perforation

To explore the colonizing bacterial flora of the nasal septum area, that is mostly afflicted by perforations, 101 healthy police students had swab samples taken from that location. The described culture strategy recovered positive cultures from 95% of the test subjects and from 60% with more than one organism. In total, 191 bacterial isolates were classified according to colony morphology, Gram-stain and a panel of standard laboratory techniques. A part of the bacteria was identified to species-level by biochemical methods and by sequencing of the 16S rRNA gene. The predominant finding was Gram-positive irregular rods - 65 presumptive Corynebacterium isolates, both lipophilic and non-lipophilic, and 37 anaerobic Propionibacterium isolates. The second largest bacterial group was Gram-positive catalase-positive cocci, of which 13 isolates were identified as Staphylococcus aureus and 53 as coagulase-negative staphylococci. The few potential airway pathogens included Streptococcus pneumonia (n = 1) and Moraxella catarrhalis (n = 3) isolates. The bacterial flora colonizing the nasal septum mainly consists of Gram-positive bacteria. Although of low virulence, the microbial flora may impact on occlusion treatment of nasal septum perforations with silicone obturators.     

Spatial and temporal variability of bacterial communities in high alpine water spring sediments

Water springs are complex, fragile and taxa-rich environments, especially in highly dynamic ecosystems such as glacier forefields experiencing glacier retreat. Bacterial communities are important actors in alpine water body metabolism, and have shown both high seasonal and spatial variations. Seven springs from a high alpine valley (Matsch Valley, South Tyrol, Italy) were examined via a multidisciplinary approach using both hydrochemical and microbiological techniques. Amplified ribosomal intergenic spacer analysis (ARISA) and electric conductivity (EC) measurements, as well as elemental composition and water stable isotopic analyses, were performed. Our target was to elucidate whether and how bacterial community structure is influenced by water chemistry, and to determine the origin and extent of variation in space and time. There existed variations in both space and time for all variables measured. Diversity values more markedly differed at the beginning of summer and then at the end; the extent of variation in space was prevalent over the time scale. Bacterial community structural variation responded to hydrochemical parameter changes; moreover, the stability of the hydrochemical parameters played an important role in shaping distinctive bacterial communities.     

Ecology and evolution in microbial systems: the generation and maintenance of diversity in phage-host interactions

Insights gained from studying the interactions between viruses and bacteria have important implications for the ecology and evolution of virus–host interactions in many environments and for pathogen–host and predator–prey interactions in general. Here, we focus on the generation and maintenance of diversity, highlighting recent laboratory and field experiments with microorganisms.     

Evaluating the use of diversity indices to distinguish between microbial communities with different traits

Several measures of biodiversity are commonly used to describe microbial communities, analyzed using 16S gene sequencing. A wide range of available experiments on 16S gene sequencing allows us to present a framework for a comparison of various diversity indices. The criterion for the comparison is the statistical significance of the difference in index values for microbial communities with different traits, within the same experiment.The results of the evaluation indicate that Shannon diversity is the most effective measure among the commonly used diversity indices. The results also indicate that, within the present framework, the Gini coefficient as a diversity index is comparable to Shannon diversity, despite the fact that the Gini coefficient, as a diversity estimator, is far less popular in microbiology than several other measures.     

Use of pyrosequencing to explore the benthic bacterial community structure in a river impacted by wastewater treatment plant discharges

In this study, we determined the diversity and composition of benthic bacterial communities collected in river sediments upstream and downstream from a wastewater treatment plant (WWTP). Pyrosequencing of bacterial 16S rRNA genes revealed notable differences between the communities from upstream and downstream sites. In particular, a higher relative abundance of Acidobacteria, Chloroflexi, Deltaproteobacteria and Firmicutes and a lower proportion of Gammaproteobacteria and Verrucomicrobia sequences were detected at the downstream site compared to the upstream site. These findings represent a first approximation of the impact of WWTP discharges on environmental microbial communities.     

Immune-directed support of rich microbial communities in the gut has ancient roots

The animal gut serves as a primary location for the complex host–microbe interplay that is essential for homeostasis and may also reflect the types of ancient selective pressures that spawned the emergence of immunity in metazoans. In this review, we present a phylogenetic survey of gut host–microbe interactions and suggest that host defense systems arose not only to protect tissue directly from pathogenic attack but also to actively support growth of specific communities of mutualists. This functional dichotomy resulted in the evolution of immune systems much more tuned for harmonious existence with microbes than previously thought, existing as dynamic but primarily cooperative entities in the present day. We further present the protochordate Ciona intestinalis as a promising model for studying gut host-bacterial dialogue. The taxonomic position, gut physiology and experimental tractability of Ciona offer unique advantages in dissecting host–microbe interplay and can complement studies in other model systems.     

Phenotypic spectrum of autosomal recessive Keratitis-Ichthyosis-Deafness Syndrome (KIDAR) due to mutations in AP1B1

Inborn errors in copper metabolism result in a diverse set of abnormalities such as Wilson disease and MEDNIK syndrome. Homozygous pathogenic variants in AP1B1 lead to KIDAR (Keratitis-Ichthyosis-Deafness Syndrome). The main phenotypic features of KIDAR are ichthyosis, keratitis, erythroderma, and progressive hearing loss accompanied by developmental delay and failure to thrive. Herein, we describe a six-and-a-half-year-old boy with KIDAR caused by a novel pathogenic variant in AP1B1 (NM_001127.4:c.1263C > A, p.Tyr421*). The proband presented with ichthyosis, erythroderma, palmoplantar keratoderma, hearing loss, and corneal scarring. He also had hypotonia, global developmental delay, and photophobia. Lastly, we review all of the previously reported cases and the clinical features associated with KIDAR.     

Medical bioremediation: prospects for the application of microbial catabolic diversity to aging and several major age-related diseases

Several major diseases of old age, including atherosclerosis, macular degeneration and neurodegenerative diseases are associated with the intracellular accumulation of substances that impair cellular function and viability. Moreover, the accumulation of lipofuscin, a substance that may have similarly deleterious effects, is one of the most universal markers of aging in postmitotic cells. Reversing this accumulation may thus be valuable, but has proven challenging, doubtless because substances resistant to cellular catabolism are inherently hard to degrade. We suggest a radically new approach: augmenting humans' natural catabolic machinery with microbial enzymes. Many recalcitrant organic molecules are naturally degraded in the soil. Since the soil in certain environments - graveyards, for example - is enriched in human remains but does not accumulate these substances, it presumably harbours microbes that degrade them. The enzymes responsible could be identified and engineered to metabolise these substances in vivo. Here, we survey a range of such substances, their putative roles in age-related diseases and the possible benefits of their removal. We discuss how microbes capable of degrading them can be isolated, characterised and their relevant enzymes engineered for this purpose and ways to avoid potential side-effects.     

The regulation of host cellular and gut microbial metabolism in the development and prevention of colorectal cancer

Metabolism regulation is crucial in colorectal cancer (CRC) and has emerged as a remarkable field currently. The cellular metabolism of glucose, amino acids and lipids in CRC are all reprogrammed. Each of them changes tumour microenvironment, modulates bacterial composition and activity, and eventually promotes CRC development. Metabolites such as short chain fatty acids, secondary bile acids, N-nitroso compounds, hydrogen sulphide, polyphenols and toxins like fragilysin, FadA, cytolethal distending toxin and colibactin play a dual role in CRC. The relationship of gut microbe-metabolite is essential in remodelling intestinal microbial ecology composition and metabolic activity. It regulates the metabolism of colonic epithelial cells and changes the tumour microenvironment in CRC. Microbial metabolism manipulation has been considered to be potentially preventive in CRC, but more large-scale clinical trials are required before their application in clinical practice in the near future.