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Concept: Human flora

202

The human gut harbors thousands of bacterial taxa. A profusion of metagenomic sequence data has been generated from human stool samples in the last few years, raising the question of whether more taxa remain to be identified. We assessed metagenomic data generated by the Human Microbiome Project Consortium to determine if novel taxa remain to be discovered in stool samples from healthy individuals. To do this, we established a rigorous bioinformatics pipeline that uses sequence data from multiple platforms (Illumina GAIIX and Roche 454 FLX Titanium) and approaches (whole-genome shotgun and 16S rDNA amplicons) to validate novel taxa. We applied this approach to stool samples from 11 healthy subjects collected as part of the Human Microbiome Project. We discovered several low-abundance, novel bacterial taxa, which span three major phyla in the bacterial tree of life. We determined that these taxa are present in a larger set of Human Microbiome Project subjects and are found in two sampling sites (Houston and St. Louis). We show that the number of false-positive novel sequences (primarily chimeric sequences) would have been two orders of magnitude higher than the true number of novel taxa without validation using multiple datasets, highlighting the importance of establishing rigorous standards for the identification of novel taxa in metagenomic data. The majority of novel sequences are related to the recently discovered genus Barnesiella, further encouraging efforts to characterize the members of this genus and to study their roles in the microbial communities of the gut. A better understanding of the effects of less-abundant bacteria is important as we seek to understand the complex gut microbiome in healthy individuals and link changes in the microbiome to disease.

Concepts: Archaea, Health, Bacteria, Gut flora, Microbiology, Full genome sequencing, Microorganism, Human flora

186

Bacterial vaginosis is a common vaginal infection, causing an abnormal vaginal discharge and/or odour in up to 50% of sufferers. Recurrence is common following recommended treatment. There are limited data on women’s experience of bacterial vaginosis, and the impact on their self-esteem, sexual relationships and quality of life. The aim of this study was to explore the experiences and impact of recurrent bacterial vaginosis on women.

Concepts: Sexual intercourse, Philosophy of science, Gynecology, Vagina, Candidiasis, Bacterial vaginosis, Human flora, Vaginitis

164

Microbial communities are important to human health. Bacterial vaginosis (BV) is a disease associated with the vagina microbiome. While the causes of BV are unknown, the microbial community in the vagina appears to play a role. We use three different machine-learning techniques to classify microbial communities into BV categories. These three techniques include genetic programming (GP), random forests (RF), and logistic regression (LR). We evaluate the classification accuracy of each of these techniques on two different datasets. We then deconstruct the classification models to identify important features of the microbial community. We found that the classification models produced by the machine learning techniques obtained accuracies above 90% for Nugent score BV and above 80% for Amsel criteria BV. While the classification models identify largely different sets of important features, the shared features often agree with past research.

Concepts: Genetics, Archaea, Microbiology, Machine learning, Vagina, Candidiasis, Bacterial vaginosis, Human flora

148

Pyrosequencing analysis of intestinal microflora from healthy Thai vegetarians and non-vegetarians exhibited 893 OTUs covering 189 species. The strong species indicator of vegetarians and non-vegetarians were Prevotella copri and Bacteroides vulgatus as well as bacterium closed to Escherichia hermanii with % relative abundance of 16.9 and 4.5-4.7, respectively. Core gut microbiota of vegetarian and non-vegetarian group consisted of 11 and 20 different bacterial species, respectively, belonging to Actinobacteria, Firmicutes and Proteobacteria commonly found in both groups. Two species of Faecalibacterium prausnitzii and Gemmiger formicilis had prevalence of 100% in both groups. Three species of Clostridium nexile, Eubacterium eligens and P. copri showed up in most vegetarians while more diversity of Collinsella aerofaciens, Ruminococcus torques, various species of Bacteroides, Parabacteroides, Escherichia, different species of Clostridium and Eubacterium were found in most non-vegetarians. Considering the correlation of personal characters, consumption behavior and microbial groups, the age of non-vegetarians showed strong positive correlation coefficient of 0.54 (p=0.001) to Bacteroides uniformis while exhibited a moderate ones to Alistipes finegoldii and B. vulgatus. Only positive moderate correlation of body mass index (BMI) and Parabacteroides distasonis appeared. Based on significant abundance of potential pathogens, the microbiota of non-vegetarian group showed the abundance of potential pathogen varieties of Bilophila wadsworthia, Escherichia coli and E. hermannii while the one of vegetarian served for only Klebsiella pneumonia. These results implied that the microbiota of vegetarian with high abundance of P. copri and low potential pathogen variety would be a way to maintain healthy in Thai.

Concepts: Bacteria, Gut flora, Microbiology, Pneumonia, Escherichia coli, Enterobacteriaceae, Firmicutes, Human flora

141

Desquamative inflammatory vaginitis is a poorly understood chronic vaginitis with an unknown etiology. Symptoms of desquamative inflammatory vaginitis include copious yellowish discharge, vulvovaginal discomfort, and dyspareunia. Cervical ectropion, the presence of glandular columnar cells on the ectocervix, has not been reported as a cause of desquamative inflammatory vaginitis. Although cervical ectropion can be a normal clinical finding, it has been reported to cause leukorrhea, metrorrhagia, dyspareunia, and vulvovaginal irritation. Patients with cervical ectropion and desquamative inflammatory vaginitis are frequently misdiagnosed with candidiasis or bacterial vaginosis and repeatedly treated without resolution of symptoms. We report the case of a 34-year-old woman with a 4-year history of profuse yellowish discharge and dyspareunia. Upon presentation, her symptoms and laboratory results met the criteria for desquamative inflammatory vaginitis, but the standard treatments did not provide long-lasting relief. As a last resort, cryotherapy (cryosurgery) of her cervix was performed for treatment of her cervical ectropion, which provided complete resolution of her symptoms. Mitchell L, King M, Brillhart H, Goldstein A. Cervical Ectropion May Be a Cause of Desquamative Inflammatory Vaginitis. Sex Med 2017;X:XX-XX.

Concepts: Epithelium, Gynecology, Cervix, Vagina, Candidiasis, Bacterial vaginosis, Human flora, Vaginitis

109

The gut microbiota regulates T cell functions throughout the body. We hypothesized that intestinal bacteria impact the pathogenesis of multiple sclerosis (MS), an autoimmune disorder of the CNS and thus analyzed the microbiomes of 71 MS patients not undergoing treatment and 71 healthy controls. Although no major shifts in microbial community structure were found, we identified specific bacterial taxa that were significantly associated with MS. Akkermansia muciniphila and Acinetobacter calcoaceticus, both increased in MS patients, induced proinflammatory responses in human peripheral blood mononuclear cells and in monocolonized mice. In contrast, Parabacteroides distasonis, which was reduced in MS patients, stimulated antiinflammatory IL-10-expressing human CD4(+)CD25(+) T cells and IL-10(+)FoxP3(+) Tregs in mice. Finally, microbiota transplants from MS patients into germ-free mice resulted in more severe symptoms of experimental autoimmune encephalomyelitis and reduced proportions of IL-10(+) Tregs compared with mice “humanized” with microbiota from healthy controls. This study identifies specific human gut bacteria that regulate adaptive autoimmune responses, suggesting therapeutic targeting of the microbiota as a treatment for MS.

Concepts: Immune system, Archaea, Bacteria, Gut flora, Microbiology, Multiple sclerosis, Autoimmunity, Human flora

86

High proportions of autistic children suffer from gastrointestinal (GI) disorders, implying a link between autism and abnormalities in gut microbial functions. Increasing evidence from recent high-throughput sequencing analyses indicates that disturbances in composition and diversity of gut microbiome are associated with various disease conditions. However, microbiome-level studies on autism are limited and mostly focused on pathogenic bacteria. Therefore, here we aimed to define systemic changes in gut microbiome associated with autism and autism-related GI problems. We recruited 20 neurotypical and 20 autistic children accompanied by a survey of both autistic severity and GI symptoms. By pyrosequencing the V2/V3 regions in bacterial 16S rDNA from fecal DNA samples, we compared gut microbiomes of GI symptom-free neurotypical children with those of autistic children mostly presenting GI symptoms. Unexpectedly, the presence of autistic symptoms, rather than the severity of GI symptoms, was associated with less diverse gut microbiomes. Further, rigorous statistical tests with multiple testing corrections showed significantly lower abundances of the genera Prevotella, Coprococcus, and unclassified Veillonellaceae in autistic samples. These are intriguingly versatile carbohydrate-degrading and/or fermenting bacteria, suggesting a potential influence of unusual diet patterns observed in autistic children. However, multivariate analyses showed that autism-related changes in both overall diversity and individual genus abundances were correlated with the presence of autistic symptoms but not with their diet patterns. Taken together, autism and accompanying GI symptoms were characterized by distinct and less diverse gut microbial compositions with lower levels of Prevotella, Coprococcus, and unclassified Veillonellaceae.

Concepts: Bacteria, Gut flora, Microbiology, Biotechnology, Pathogen, Autism, Pathogenic bacteria, Human flora

47

Vultures are scavengers that fill a key ecosystem niche, in which they have evolved a remarkable tolerance to bacterial toxins in decaying meat. Here we report the first deep metagenomic analysis of the vulture microbiome. Through face and gut comparisons of 50 vultures representing two species, we demonstrate a remarkably conserved low diversity of gut microbial flora. The gut samples contained an average of 76 operational taxonomic units (OTUs) per specimen, compared with 528 OTUs on the facial skin. Clostridia and Fusobacteria, widely pathogenic to other vertebrates, dominate the vulture’s gut microbiota. We reveal a likely faecal-oral-gut route for their origin. DNA of prey species detectable on facial swabs was completely degraded in the gut samples from most vultures, suggesting that the gastrointestinal tracts of vultures are extremely selective. Our findings show a strong adaption of vultures and their bacteria to their food source, exemplifying a specialized host-microbial alliance.

Concepts: Archaea, Bacteria, Gut flora, Microbiology, Species, Bird, Vulture, Human flora

32

In complex biological systems, small molecules often mediate microbe-microbe and microbe-host interactions. Using a systematic approach, we identified 3,118 small-molecule biosynthetic gene clusters (BGCs) in genomes of human-associated bacteria and studied their representation in 752 metagenomic samples from the NIH Human Microbiome Project. Remarkably, we discovered that BGCs for a class of antibiotics in clinical trials, thiopeptides, are widely distributed in genomes and metagenomes of the human microbiota. We purified and solved the structure of a thiopeptide antibiotic, lactocillin, from a prominent member of the vaginal microbiota. We demonstrate that lactocillin has potent antibacterial activity against a range of Gram-positive vaginal pathogens, and we show that lactocillin and other thiopeptide BGCs are expressed in vivo by analyzing human metatranscriptomic sequencing data. Our findings illustrate the widespread distribution of small-molecule-encoding BGCs in the human microbiome, and they demonstrate the bacterial production of drug-like molecules in humans. PAPERCLIP:

Concepts: DNA, Archaea, Bacteria, Gut flora, Microbiology, Escherichia coli, Pathogen, Human flora

30

Our intestinal microbiota harbours a diverse bacterial community required for our health, sustenance and wellbeing. Intestinal colonization begins at birth and climaxes with the acquisition of two dominant groups of strict anaerobic bacteria belonging to the Firmicutes and Bacteroidetes phyla. Culture-independent, genomic approaches have transformed our understanding of the role of the human microbiome in health and many diseases. However, owing to the prevailing perception that our indigenous bacteria are largely recalcitrant to culture, many of their functions and phenotypes remain unknown. Here we describe a novel workflow based on targeted phenotypic culturing linked to large-scale whole-genome sequencing, phylogenetic analysis and computational modelling that demonstrates that a substantial proportion of the intestinal bacteria are culturable. Applying this approach to healthy individuals, we isolated 137 bacterial species from characterized and candidate novel families, genera and species that were archived as pure cultures. Whole-genome and metagenomic sequencing, combined with computational and phenotypic analysis, suggests that at least 50-60% of the bacterial genera from the intestinal microbiota of a healthy individual produce resilient spores, specialized for host-to-host transmission. Our approach unlocks the human intestinal microbiota for phenotypic analysis and reveals how a marked proportion of oxygen-sensitive intestinal bacteria can be transmitted between individuals, affecting microbiota heritability.

Concepts: Archaea, Bacteria, Gut flora, Evolution, Microbiology, Escherichia coli, Human flora, Bacteroidetes