March 15, 2018

A few interesting articles in early life human microbiome, plus:
A comparison between Staphylococcus epidermidis commensal and pathogenic lineages from the skin of healthy individuals living in North American and India; A new tool to reconstruct microbial genome-scale metabolic models (GSMMs) from their genome sequence; The seasonal changes in Amazon rainforest soil microbiome are associated with changes in the canopy; A specific class of chemicals secreted by birds modulates their feather microbiome; chronic stress alters gut microbiota and triggers a specific immune response in a mouse model of colitis; and evidence that the short chain fatty acids profile in the gut reflects the impact of dietary fibre on the microbiome using the PolyFermS continuous intestinal fermentation model.

Pregnancy and early life

*Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium – Terhi Tapiainen – Pediatric Research

*Bifidobacterium longum subsp infantis CECT7210 supplemented formula reduces diarrhoea in healthy infants: a randomized controlled trial – Joaquin Escribano – Pediatric Research

*Gut microbiota in adolescents and the association with fatty liver: The EPOCH study – Maggie A Stanislawski – Pediatric Research

Review: Does Dysbiosis in Intestinal Microbiome Plays a Role in Children with Relapsing Idiopathic Nephrotic Syndrome? – Crespo-Salgado J. – American Journal of Nephrology

Gut Microbiota Dysbiosis in Children with Relapsing Idiopathic Nephrotic Syndrome – Tsuji S – American Journal of Nephrology

Human skin microbiome

*Phylogenomic Based Comparative Studies on Indian and American Commensal Staphylococcus epidermidis Isolates – Shikha Sharma – Frontiers in Microbiology

Human oral microbiome

Unusual oral mucosal microbiota after hematopoietic cell transplantation with glycopeptide antibiotics: potential association with pathophysiology of oral mucositis – Misato Muro – Folia Microbiologica

Supragingival and subginival microbiota from patients with poor oral hygiene submitted to radiotherapy for head and neck cancer treatment – Elerson Gaetti-Jardim Jr – Archives of Oral Biology

Human nearly-sterile sites

PrePrint: Transcriptome analysis in whole blood reveals increased microbial 1 diversity in schizophrenia – Loes M Olde Loohuis – bioRxiv

Human gut microbiome

Investigations on the interplays between Schistosoma mansoni, praziquantel and the gut microbiome – Pierre H. H. Schneeberger – Parasites and Vectors

FUT2 genotype and secretory status are not associated with fecal microbial composition and inferred function in healthy subjects – Williams Turpin – Gut Microbes

Bacterial growth, flow, and mixing shape human gut microbiota density and composition – Markus Arnoldini – Gut Microbes

Complementary effects of cereal and pulse polyphenols and dietary fiber on chronic inflammation and gut health – Joseph M. Awika – Food & Function

Roseburia intestinalis alleviates experimental colitis pathology by inducing anti-inflammatory responses – Zhaohua Shen – Gastroenterology and Hepatology

Targeting gut microbiota in hepatocellular carcinoma: probiotics as a novel therapy – Murphy L. Y. Wan – Hepatobiliary Surgery and Nutrition

Fecal Microbiota Signatures Are Associated with Response to Ustekinumab Therapy among Crohn’s Disease Patients – Matthew K. Doherty – mBio

Disruption of the Gut Microbiota With Antibiotics Exacerbates Acute Vascular Rejection
Kevin Rey – Transplantation

Review: Multiple hit infection and autoimmunity: the dysbiotic microbiota–ACPA connection in rheumatoid arthritis – Lazaros I Sakkas – Current Opinion in Rheumatology

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In vitro experiments

*Understanding the prebiotic potential of different dietary fibers using an in vitro continuous adult fermentation model (PolyFermS) – Sophie A. Poeker – Scientific Reports

Animal experiments

Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites – Shiho Fujisaka – Cell Reports

Fructose liquid and solid formulations differently affect gut integrity, microbiota composition and related liver toxicity: a comparative in vivo study – Raffaella Mastrocola – Journal of Nutritional Biochemistry

NLRX1 Modulates Immunometabolic Mechanisms Controlling the Host–Gut Microbiota Interactions during Inflammatory Bowel Disease – Andrew Leber – Frontiers in Immunology

Tapering Courses of Oral Vancomycin Induce Persistent Disruption of the Microbiota that Provide Colonization Resistance to Clostridium difficile and Vancomycin-Resistant Enterococci in Mice – Myreen E. Tomas – Antimicrobial Agents and Chemotherapy

The Lung Microbiota of Healthy Mice are Highly Variable, Cluster by Environment, and Reflect Variation in Baseline Lung Innate Immunity – Robert P. Dickson – American Journal of Respiratory and Critical Care Medicine

Interactions between stress and sex in microbial responses within the microbiota-gut-brain axis to stress in a mouse model – Matthew C.B. Tsilimigras – Psychosomatic Medicine

*Chronic stress promotes colitis by disturbing the gut microbiota and triggering immune system response – Xinghua Gao – PNAS

Modulation of inflammatory arthritis by gut microbiota through mucosal inflammation and autoantibody generation – Widian K. Jubair – Arthritis & Rheumatology

Genetic Markers Are Associated with the Ruminal Microbiome and Metabolome in Grain and Sugar Challenged Dairy Heifers – Helen M. Golder

Animal microbiome

Gut microbes limit growth in house sparrow nestlings (Passer domesticus) but not through limitations in digestive capacity – Kevin D. Kohl – Integrative Zoology

*Chemical regulation of body feather microbiota in a wild bird – Staffan Jacob – Molecular Ecology

Plant, root, and soil microbiome

Bacterial community changes in response to oil contamination and perennial crop cultivation – Lijuan Yan – Environmental Science and Pollution Research

Integrated network analysis reveals the importance of microbial interactions for maize growth – Jiemeng Tao – Applied Microbiology and Biotechnology

*Spatio-temporal dynamics of soil bacterial communities as a function of Amazon forest phenology – Erika Buscardo – Scientific Reports

Microbiome dynamics during ensiling of corn with and without Lactobacillus plantarum inoculant – Jitendra Keshridf – Applied Microbiology and Biotechnology

Barcoded Pyrosequencing Reveals a Shift in the Bacterial Community in the Rhizosphere and Rhizoplane of Rehmannia glutinosa under Consecutive Monoculture – Linkun Wu – International Journal of Molecular Sciences

Chrysomya megacephala larvae feeding favourably influences manure microbiome, heavy metal stability and greenhouse gas emissions – Xiaoyun Wang – Microbial Biotechnology

Water and extremophile microbiome

Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community – Laura Gómez-Consarnau – bioRxiv

Microbial Ecology

Mycotoxin: Its Impact on Gut Health and Microbiota – Winnie-Pui-Pui Liew – Frontiers in Cellular and Infection Microbiology

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Probiotics / prebiotics

Effect of an Enterococcus faecium probiotic on specific IgA following live Salmonella Enteritidis vaccination of layer chickens – Breno C. B. Beirão – Avian Pathology

Effect of a Protein Supplement on the Gut Microbiota of Endurance Athletes: A Randomized, Controlled, Double-Blind Pilot Study – Diego Moreno-Pérez – Nutrients

Fecal Transplants

Fecal transplants in spondyloarthritis and uveitis: ready for a clinical trial? – Rene Y Choi – Current Opinion in Rheumatology

Phages and viruses

Together Forever: Bacterial–Viral Interactions in Infection and Immunity – Zhenda Shi – Viruses

Bioinformatics

*Towards predicting the environmental metabolome from metagenomics with a mechanistic model – Daniel R. Garza – Nature Microbiology

Phylogenetic convolutional neural networks in metagenomics – Diego Fioravanti – BMC Bioinformatics

Waste and Pollution

Illumina MiSeq Sequencing reveals microbial community in HA process for dyeing wastewater treatment fed with different co-substrates – Xuehui Xie – Chemosphere

Techniques

Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis – Jocelyn Sietsma Penington – Scientific Reports

Direct detection of Coccidioides from Arizona soils using CocciENV, a highly sensitive and specific real-time PCR assay – J R Bowers – Medical Mycology

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