Bioinformatics and holobiota
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The symbiotic intestinal ciliates and the evolution of their hosts

An extensive study on excrement and rumen fluids in plant-eating mammals from all over the whole world shows that the ciliates in their guts have evolved in parallel with them.

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gut protists

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Genome Medicine

Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet
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Diminution of the gut resistome after a gut microbiota-targeted dietary intervention in obese children

Diminution of the gut resistome after a gut microbiota-targeted dietary intervention in obese children | Bioinformatics and holobiota | Scoop.it
antly diminished the gut resistome and alleviated metabolic syndrome in obese children. Of the non-redundant metagenomic gene catalog of ~2 × 106 microbial genes, 399 ARGs were identified in 131 gene types a
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Helicobacter pylori Eradication Causes Perturbation of the Human Gut Microbiome in Young Adults

Accumulating evidence shows that Helicobacter pylori protects against some metabolic and immunological diseases in which the development of these diseases coincide with temporal or permanent dysbiosis. The aim of this study was to assess the effect of H . pylori eradication on the human gut microbiome. Methods As part of the currently on-going ESSAY (Eradication Study in Stable Adults/Youths) study, we collected stool samples from 17 H . pylori -positive young adult (18–30 years-old) volunteers. The same cohort was followed up 6, 12 and 18 months-post H . pylori eradication. The impact of H . pylori on the human gut microbiome pre- and post-eradication was investigated using high throughput 16S rRNA gene (V3-V4 region) sequencing using the Illumina Miseq followed by data analysis using Qiime pipeline. Results We compared the composition and diversity of bacterial communities in the fecal microbiome of the H . pylori -positive volunteers, before and after H . pyl ori eradication therapy. The 16S rRNA gene was sequenced at an average of 150,000–170,000 reads/sample. The microbial diversity were similar pre- and post- H . pylori eradication with no significant differences in richness and evenness of bacterial species. Despite that the general profile of the gut microbiome was similar pre- and post-eradication, some changes in the bacterial communities at the phylum and genus levels were notable, particularly the decrease in relative abundance of Bacterioidetes and corresponding increase in Firmicutes after H . pylori eradication. The significant increase of short-chain fatty acids (SCFA)-producing bacteria genera could also be associated with increased risk of metabolic disorders. Conclusions Our preliminary stool metagenomics study shows that eradication of H . pylori caused perturbation of the gut microbiome and may indirectly affect the health of human. Clinicians should be aware of the effect of broad spectrum antibiotics used in H . pylori eradication regimen and be cautious in the clinical management of H . pylori infection, particularly in immunocompromised patients.

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Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children 

Malnutrition in children is a persistent challenge that is not always remedied by improvements in nutrition. This is because a characteristic community of gut microbes seems to mediate some of the pathology. Human gut microbes can be transplanted effectively into germ-free mice to recapitulate their associated phenotypes. Using this model, Blanton et al. found that the microbiota of healthy children relieved the harmful effects on growth caused by the microbiota of malnourished children. In infant mammals, chronic undernutrition results in growth hormone resistance and stunting. In mice, Schwarzer et al. showed that strains of Lactobacillus plantarum in the gut microbiota sustained growth hormone activity via signaling pathways in the liver, thus overcoming growth hormone resistance. Together these studies reveal that specific beneficial microbes could potentially be exploited to resolve undernutrition syndromes.
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J Gordon
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The ISME Journal - Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes

The ISME Journal - Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes | Bioinformatics and holobiota | Scoop.it
Resident gut microbes co-exist with transient bacteria to form the gut microbiota. Despite increasing evidence suggesting a role for transient microbes on gut microbiota function, the interplay between resident and transient members of this microbial community is poorly defined. We aimed to determine the extent to which a host’s autochthonous gut microbiota influences niche permissivity to transient bacteria using a fermented milk product (FMP) as a vehicle for five food-borne bacterial strains. Using conventional and gnotobiotic rats and gut microbiome analyses (16S rRNA genes pyrosequencing and reverse transcription qPCR), we demonstrated that the clearance kinetics of one FMP bacterium, Lactococcus lactis CNCM I-1631, were dependent on the structure of the resident gut microbiota. Susceptibility of the resident gut microbiota to modulation by FMP intervention correlated with increased persistence of L. lactis. We also observed gut microbiome configurations that were associated with altered stability upon exposure to transient bacteria. Our study supports the concept that allochthonous bacteria have transient and subject-specific effects on the gut microbiome that can be leveraged to re-engineer the gut microbiome and improve dysbiosis-related diseases.
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Biogeography of a human oral microbiome at the micron scale

Biogeography of a human oral microbiome at the micron scale | Bioinformatics and holobiota | Scoop.it

The physiology and ecology of complex microbial communities are strongly dependent on the immediate surroundings of each microbe, including the identity of neighboring microbes; however, information on the micron-scale organization of microbiomes is largely lacking. Using sequencing data combined with spectral fluorescence imaging, we have discovered a multigenus, highly organized microbial consortium in human dental plaque. The spatial structure of the consortium reveals unanticipated interactions and provides a framework for understanding the organization, metabolism, and systems biology of the microbiome and ultimately, its effect on the health of the human host. Our synthesis of high-throughput sequencing data with spatial and structural information shows the informative value of microbial biogeography at the micron scale.

 
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fluoro forest

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Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis : Nature Communications : Nature Publishing Group

Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis : Nature Communications : Nature Publishing Group | Bioinformatics and holobiota | Scoop.it
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Proton pump inhibitors affect the gut microbiome -- Imhann et al. -- Gut

Proton pump inhibitors affect the gut microbiome -- Imhann et al. -- Gut | Bioinformatics and holobiota | Scoop.it
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Gut Microbiota Orchestrates Energy Homeostasis during Cold: Cell

Gut Microbiota Orchestrates Energy Homeostasis during Cold: Cell | Bioinformatics and holobiota | Scoop.it
Cold exposure leads to marked changes in the gut microbiota composition•Cold microbiota transplantation increases insulin sensitivity and WAT browning•Cold exposure or cold transplantation increase the gut size and absorptive capacity•Reconstitution of cold-suppressed A. muciniphila reverts the increased caloric uptake
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Associations between human milk oligosaccharides and infant body composition in the first 6 mo of life

Design: Twenty-five mother-infant dyads were recruited from the University Hospital at the University of Oklahoma Health Sciences Center. Infants were breastfed for 6 mo. Breast-milk and infant measures were obtained at 1 and 6 mo of infant age. HMO composition was analyzed by high-pressure liquid chromatography, and infant growth (length and weight) and body composition (percentage fat, total fat, lean mass) were measured by dual-energy X-ray absorptiometry. Relations between HMOs and infant growth and body composition were examined by using multiple linear regression. A priori covariates included maternal prepregnancy body mass index, pregnancy weight gain, and infant age and sex.

 
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spectrum of oligosaccharides in mother milk - that feed only microbiota - correlate with infant growth

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Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease | Bioinformatics and holobiota | Scoop.it

Inflammation, antibiotics, and diet independently affect microbiota in Crohn’s disease

Antibiotics are associated with bacterial dysbiosis and increased fungi

Dysbiosis decreases with reduction in intestinal inflammation

Diet has an independent and rapid effect on gut microbiota composition

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Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans | Bioinformatics and holobiota | Scoop.it
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Birth mode-dependent association between pre-pregnancy maternal weight status and the neonatal intestinal microbiome

Birth mode-dependent association between pre-pregnancy maternal weight status and the neonatal intestinal microbiome | Bioinformatics and holobiota | Scoop.it
The intestinal microbiome is a unique ecosystem that influences metabolism in humans. Experimental evidence indicates that intestinal microbiota can transfer an obese phenotype from humans to mice. Since mothers transmit intestinal microbiota to their offspring during labor, we hypothesized that among vaginal deliveries, maternal body mass index is associated with neonatal gut microbiota composition. We report the association of maternal pre-pregnancy body mass index on stool microbiota from 74 neonates, 18 born vaginally (5 to overweight or obese mothers) and 56 by elective C-section (26 to overweight or obese mothers). Compared to neonates delivered vaginally to normal weight mothers, neonates born to overweight or obese mothers had a distinct gut microbiota community structure (weighted UniFrac distance PERMANOVA, p < 0.001), enriched in Bacteroides and depleted in Enterococcus, Acinetobacter, Pseudomonas, and Hydrogenophilus. We show that these microbial signatures are predicted to result in functional differences in metabolic signaling and energy regulation. In contrast, among elective Cesarean deliveries, maternal body mass index was not associated with neonatal gut microbiota community structure (weighted UniFrac distance PERMANOVA, p = 0.628). Our findings indicate that excess maternal pre-pregnancy weight is associated with differences in neonatal acquisition of microbiota during vaginal delivery, but not Cesarean delivery. These differences may translate to altered maintenance of metabolic health in the offspring.
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Recovering complete and draft population genomes from metagenome datasets

Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.

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Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants

Necrotizing enterocolitis (NEC) afflicts approximately 10% of extremely preterm infants with high fatality. Inappropriate bacterial colonization with Enterobacteriaceae is implicated, but no specific pathogen has been identified. We identify uropathogenic E. coli (UPEC) colonization as a significant risk factor for the development of NEC and subsequent mortality. We describe a large-scale deep shotgun metagenomic sequence analysis of the early intestinal microbiome of 144 preterm and 22 term infants. Using a pan-genomic approach to functionally subtype the E. coli, we identify genes associated with NEC and mortality that indicate colonization by UPEC. Metagenomic multilocus sequence typing analysis further defined NEC-associated strains as sequence types often associated with urinary tract infections, including ST69, ST73, ST95, ST127, ST131, and ST144. Although other factors associated with prematurity may also contribute, this report suggests a link between UPEC and NEC and indicates that further attention to these sequence types as potential causal agents is needed.
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The microbiome of uncontacted Amerindians

Most studies of the human microbiome have focused on westernized people with life-style practices that decrease microbial survival and transmission, or on traditional societies that are currently in transition to westernization. We characterize the fecal, oral, and skin bacterial microbiome and resistome of members of an isolated Yanomami Amerindian village with no documented previous contact with Western people. These Yanomami harbor a microbiome with the highest diversity of bacteria and genetic functions ever reported in a human group. Despite their isolation, presumably for >11,000 years since their ancestors arrived in South America, and no known exposure to antibiotics, they harbor bacteria that carry functional antibiotic resistance (AR) genes, including those that confer resistance to synthetic antibiotics and are syntenic with mobilization elements. These results suggest that westernization significantly affects human microbiome diversity and that functional AR genes appear to be a feature of the human microbiome even in the absence of exposure to commercial antibiotics. AR genes are likely poised for mobilization and enrichment upon exposure to pharmacological levels of antibiotics. Our findings emphasize the need for extensive characterization of the function of the microbiome and resistome in remote nonwesternized populations before globalization of modern practices affects potentially beneficial bacteria harbored in the human body.
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The ISME Journal - Capturing the most wanted taxa through cross-sample correlations

The ISME Journal - Capturing the most wanted taxa through cross-sample correlations | Bioinformatics and holobiota | Scoop.it

The Human Microbiome Project (HMP) identified the 16S rRNA gene sequences of 'most wanted' taxa—prevalent in the healthy human microbiota but distant from previously known sequences. Since 2012, few of the corresponding genomes have been isolated and sequenced, and only through advanced isolation techniques. We demonstrate that the genomes of the most wanted taxa can be identified computationally through their correlation in abundance across multiple public metagenomic data sets. We link over 200 most wanted sequences with nearly complete genome sequences, including half of the taxa identified as high-priority targets by the HMP. The genomes we identify have strong similarity to genomes reconstructed through expensive isolation techniques, and provide a more complete functional characterization of these organisms than can be extrapolated from their 16S rRNA gene. We also provide insights into the function of organisms for which 16S rRNA gene signatures were recently reported to be associated with health and host genetic factors.


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The ISME Journal - High-resolution phylogenetic microbial community profiling

The ISME Journal - High-resolution phylogenetic microbial community profiling | Bioinformatics and holobiota | Scoop.it

We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structures at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification


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Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria. - PubMed - NCBI

Sci Rep. 2015 Dec 2;5:17450. doi: 10.1038/srep17450.
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Won Gi Yoo's curator insight, December 14, 2015 8:35 PM

담석증 환자의 담즙내 메타게놈 분석: 미생물들은 환자-특이적이며, 환자의 담즙은 미생물다양성을 저해.

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Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma

Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma | Bioinformatics and holobiota | Scoop.it
Alexander Tyakht's insight:

indians microbiota

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Temporal and spatial variation of the human microbiota during pregnancy

Temporal and spatial variation of the human microbiota during pregnancy | Bioinformatics and holobiota | Scoop.it

Using a case-control cohort of 40 women, we characterized weekly variation in the vaginal, gut, and oral microbiota during and after pregnancy. 


Linear mixed-effects modeling, medoid-based clustering, and Markov chain modeling were used to analyze community temporal trends, community structure, and vaginal community state transitions.


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multi-site microbiota in pregnancy

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Dysbiotic gut microbiome: A key element of Crohn's disease

Many aspects of the human immune system seem to be associated with the gut microbiome

Impaired bacterial sensing and handling are initial steps in Crohn's pathology

Presence of NOD2/ATG16L genotypes is associated with alterations of Crohn's microbiome

Relationship may exist between the host genotype and intestinal dysbiosis

Initial findings regarding therapeutic microbiome modulation are promising

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