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PLOS Computational Biology: Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

PLOS Computational Biology: Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota | Bioinformatics and holobiota | Scoop.it
PLOS Computational Biology is an open-access
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modelling gut microbiota behavior with differential equations

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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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Science: Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

We developed a method—multi-taxon INsertion Sequencing (INSeq)—for monitoring the behavior of tens of thousands of transposon (Tn) mutants of multiple bacterial species and strains simultaneously in the guts of gnotobiotic mice. We focused on four prominent human gut Bacteroides: one strain of B. cellulosilyticus, one strain of B. ovatus, and two strains of B. thetaiotaomicron. INSeq libraries, each composed of 87,000 to 167,000 isogenic Tn mutant strains, were produced (single site of Tn insertion per mutant strain; a total of 11 to 26 Tn insertions represented in the library per gene; and 82 to 92% genes covered per genome). The four mutant libraries were introduced into germ-free mice together with 11 wild-type species commonly present in the human gut microbiota. Animals were given a diet rich in fat and simple sugars but devoid of complex polysaccharides [diet 1 (D1)] or one rich in plant polysaccharides and low in fat (D2), either monotonously or in the sequence D1-D2-D1 or D2-D1-D2. Wecalculated a “fitness index” for each gene on the basis of the relative abundance of its INSeq reads in the fecal or cecal microbiota compared with the input library. In vivo INSeq data were correlated with INSeq data generated from organisms cultured under defined in vitro conditions; microbial RNA-seq profiling of the community’s metatranscriptome; and reconstructions of metabolic pathways, regulons, and polysaccharide utilization loci. On the basis of the results, we designed a prebiotic intervention.

 
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J Gordon

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BMC Microbiology | Full text | In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project’s reference genome database

In this study, we employed an in silico screening approach to mine potential bacteriocin clusters in genome-sequenced isolates from the gastrointestinal tract (GIT). More specifically, the bacteriocin genome-mining tool BAGEL3 was used to identify potential bacteriocin producers in the genomes of the GIT subset of the Human Microbiome Project’s reference genome database. Each of the identified gene clusters were manually annotated and potential bacteriocin-associated genes were evaluated.

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The ISME Journal - The initial state of the human gut microbiome determines its reshaping by antibiotics

The ISME Journal - The initial state of the human gut microbiome determines its reshaping by antibiotics | Bioinformatics and holobiota | Scoop.it

we administered a second-generation cephalosporin, cefprozil, to healthy volunteers. Stool samples gathered before antibiotic exposure, at the end of the treatment and 3 months later were analysed using shotgun metagenomic sequencing.


We show that standard antibiotic treatment can alter the gut microbiome in a specific, reproducible and predictable manner. 


Resistance genes that were not detectable prior to treatment were observed after a 7-day course of antibiotic administration. Specifically, point mutations in beta-lactamase blaCfxA-6 were enriched after antibiotic treatment in several participants. 

Alexander Tyakht's insight:

shotgun antibiotics human resistome

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[1506.05171] On the Origins and Control of Community Types in the Human Microbiome

Here we adopted a dynamic systems approach and found that heterogeneity in the interspecific interactions or the presence of strongly interacting species is sufficient to explain community types, independent of the topology of the underlying ecological network. By controlling the presence or absence of these strongly interacting species we can steer the microbial ecosystem to any desired community type.
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Structure and function of the global ocean microbiome

We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes.

Alexander Tyakht's insight:

hey Vilgelm)

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Antibiotics and the developing infant gut microbiota and resistom

Neonatal and pediatric populations routinely receive antibiotic treatment.

Disrupting the developing infant gut microbiota may have long-term metabolic consequences.

A diverse gut-associated antibiotic resistome is established early in life.

Antibiotic treatment leads to long-term enrichment of antibiotic resistance genes and promotes transfer to pathogens.

Highly sampled, longitudinal infant cohort studies and controlled mouse models of therapeutic antibiotic treatments are essential for filling knowledge gaps.

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BMC Bioinformatics | Full text | InteMAP: Integrated metagenomic assembly pipeline for NGS short reads

e developed a pipeline named InteMAP to integrate three assemblers, ABySS, IDBA-UD and CABOG, which were found to complement each other in assembling metagenomic sequences. 

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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.


Alexander Tyakht's insight:

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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A catalog of the mouse gut metagenome : Nature Biotechnology : Nature Publishing Group

We established a catalog of the mouse gut metagenome comprising ~2.6 million nonredundant genes by sequencing DNA from fecal samples of 184 mice. To secure high microbiome diversity, we used mouse strains of diverse genetic backgrounds, from different providers, kept in different housing laboratories and fed either a low-fat or high-fat diet. Similar to the human gut microbiome, >99% of the cataloged genes are bacterial. We identified 541 metagenomic species and defined a core set of 26 metagenomic species found in 95% of the mice. The mouse gut microbiome is functionally similar to its human counterpart, with 95.2% of its Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous groups in common. However, only 4.0% of the mouse gut microbial genes were shared (95% identity, 90% coverage) with those of the human gut microbiome. This catalog provides a useful reference for future studies.

 
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gene catalog

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MetaPhlAn2 for enhanced metagenomic taxonomic profiling : Nature Methods : Nature Publishing Group

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In vivo imaging and tracking of host-microbiota interactions via metabolic labeling of gut anaerobic bacteria : Nature Medicine

We applied metabolic oligosaccharide engineering and bioorthogonal click chemistry to label various commensal anaerobes, including Bacteroides fragilis, a common and immunologically important commensal. We studied the dissemination of B. fragilis after acute peritonitis and characterized the interactions of the intact microbe and its polysaccharide components in myeloid and B cell lineages. We were able to assess the distribution and colonization of labeled B. fragilis along the intestine, as well as niche competition after coadministration of multiple species of the microbiota. We also fluorescently labeled nine additional commensals (eight anaerobic and one microaerophilic) from three phyla common in the gut—Bacteroidetes, Firmicutes and Proteobacteria—as well as one aerobic pathogen (Staphylococcus aureus). This strategy permits visualization of the anaerobic microbial niche by various methods, including intravital two-photon microscopy and non-invasive whole-body imaging, and can be used to study microbial colonization and host–microbe interactions in real time.

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wow

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Patterned progression of bacterial populations in the premature infant gut

Patterned progression of bacterial populations in the premature infant gut | Bioinformatics and holobiota | Scoop.it

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.

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La Rosa

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Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation : Nature Communications : Nature Publishing Group

Using a combination of genomics, enzymology and crystallography, we show that the mucin-degrader R. gnavus ATCC 29149 strain produces an intramolecular trans-sialidase (IT-sialidase) that cleaves off terminal α2-3-linked sialic acid from glycoproteins, releasing 2,7-anhydro-Neu5Ac instead of sialic acid. Evidence of IT-sialidases in human metagenomes indicates that this enzyme occurs in healthy subjects but is more prevalent in IBD metagenomes. Our results uncover a previously unrecognized enzymatic activity in the gut microbiota, which may contribute to the adaptation of intestinal bacteria to the mucosal environment in health and disease.

Alexander Tyakht's insight:

not all Ruminococci are nice - R. gnavus is mucus degrader enriched in IBD - here one of its arms is exposed - IT -sialidase

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Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock

the mechanism responsible for rhythmicity has not been fully clarified. Here we report that both the host circadian system and host gender influence the rhythmicity of the total load and taxonomic abundances in the fecal microbiota, and that regulation by the host clock is dominant. Disruption of the host circadian clock by deletion of Bmal1 altered the fecal microbial composition in a gender-dependent fashion. Our analyses suggest the need to consider circadian factors and host gender in the design of microbiome studies, and highlight the importance of analyzing absolute abundance in understanding the microbiota.

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