Today we have quite a long Microbiome Digest, with many papers in Human Gut , Water, Plant/Soil Microbiome and Probiotics Sections. Among many interesting papers today, check an essay by Stilianos Louca “Probing the metabolism of microorganisms” and a perspective by Cesar de la Fuente “Neuromicrobiology: how microbes influence the brain “.

Events and jobs

LabTechnician/Microbiology, Kalamazoo, MI 49001

Instructional Associate- Microbiology, Fort Worth, TX

Visiting Professor (Part Time) Microbiology Jacksonville, FL Campus

Assistant Professor in Food Microbiology/Safety, Edinburg, Texas (US)

General microbiome

Probing the metabolism of microorganisms – Stilianos Louca – Science

Pregnancy and early life

Persistence of Supplemented Bifidobacterium longum subsp. infantis EVC001 in Breastfed Infants – Steven A. Frese – mSphere

 

 

Human nearly-sterile sites 

Perspective: Neuromicrobiology: how microbes influence the brain – Cesar de la Fuente-Nunez – ACS Chemical Neuroscience

Assessment of the comparability of CLSI, EUCAST and Stokes antimicrobial susceptibility profiles for Escherichia coli uropathogenic isolates – C O’Halloran – British Journal of Biomedical Science

Human gut microbiome

Gut epithelial vitamin D receptor regulates microbiota-dependent mucosal inflammation by suppressing intestinal epithelial cell apoptosis – Lei He – Endocrinology

The long-term effects of faecal microbiota transplantation for gastrointestinal symptoms and general health in patients with recurrent Clostridium difficile infection – J. Jalanka – Alimentary Pharmacology & Therapeutics

Vitamin A deficiency in mice alters host and gut microbial metabolism leading to altered energy homeostasis – Yuan Tian – The Journal of Nutritional Biochemistry

Changes in the gut microbiota composition and the plasma ghrelin level in patients with Helicobacter pylori-infected patients with eradication therapy – Hidetaka Yanagi – Gut Microbiota

Perspectives: Gut microbiota–derived short-chain fatty acids and kidney diseases – Lingzhi Li –  Drug Design, Development and Therapy

Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota – Lesley Hoyles – bioRxiv

Changes in the gut microbiota composition and the plasma ghrelin level in patients with Helicobacter pylori-infected patients with eradication therapy  – Hidetaka Yanagi – Gut Microbiota

Enteric Microbiome Markers as Early Predictors of Clinical Outcome in Allogeneic Hematopoietic Stem Cell Transplant: Results of a Prospective Study in Adult Patients – Nicasio Mancini – Open Forum Infectious Diseases

The long-term effects of faecal microbiota transplantation for gastrointestinal symptoms and general health in patients with recurrent Clostridium difficile infection – J. Jalanka – Alimentary Pharmacology & Therapeutics

Gut Microbiota and Host Juvenile Growth – Martin Schwarzer – Calcified Tissue International

Disruption of the Gut Ecosystem by Antibiotics – Mi Young Yoon – Yonsei Med Journal

Animal experiments 

Removal of the cecum affects intestinal fermentation, enteric bacterial community structure, and acute colitis in mice – Kirsty Brown – Gut Microbes

Influenza A virus subtype H9N2 infection disrupts the composition of intestinal microbiota of chickens – Alexander Yitbarek – FEMS Microbiology Ecology

Comparision of the intestinal musocal microbiota in dogs diagnosed with idiopathic inflamatorz bowel disease and dogs with food/responsive diarrhea before and after treatement – K. Kalenyak – FEMS Microbiology Ecology

Lysine Restriction Affects Feed Intake and Amino Acid Metabolism via Gut Microbiome in Piglets – Yin J – Logo Cellular Physiology and Biochemistry

Animal microbiome

SPM-1-producing Pseudomonas aeruginosa ST277 clone recovered from microbiota of migratory birds – Willames M.B.S.Martins – Diagnostic Microbiology and Infectious Disease

Plant, root, and soil microbiome

Ravibacter arvi gen. nov., sp. nov., isolated from farmland soil during development of new culture techniques – Dhiraj Kumar Chaudhary – International Journal of Systematic and Evolutionary Microbiology

Mangrovitalea sediminis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from mangrove sediment – Hu Liao – International Journal of Systematic and Evolutionary Microbiology

Prolonged exposure does not increase soil microbial community compositional response to warming along geothermal gradients – Dajana Radujković – FEMS Microbiology Ecology

Plant–soil feedbacks promote negative frequency dependence in the coexistence of two aridland grasses – Y. Anny Chung – Proceedings of the Royal Society B

Draft genome sequence of Bacillus velezensis 2A-2B strain: a rhizospheric inhabitant of Sporobolus airoides (Torr.) Torr., with antifungal activity against root rot causing phytopathogens – Inés Martínez-Raudales – Standards in Genomic Sciences

Rhizosphere Microorganisms: Application of Plant Beneficial Microbes in Biological Control of Weeds – Satyavir S. Sindhu – Microorganisms for Green Revolution

Shifts in bacterial and fungal diversity in a paddy soil faced with phosphorus surplus – Ming Liu – Biology and Fertility of Soils

Water and extremophile microbiome

Strategies and ecological roles of algicidal bacteria – Nils Meyer – FEMS Microbiology Reviews

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations – Sarahi L. Garcia – ISME Journal

The predictability of a lake phytoplankton community, from hours to years – Mridul K. Thomas – bioRxiv

Oceaniglobus indicus gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from surface seawater –  Jianyang Li –  International Journal of Systematic and Evolutionary Microbiology

Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota – Wei Qin – International Journal of Systematic and Evolutionary Microbiology

A new niche for anoxygenic phototrophs as endoliths – Daniel Roush – Applied and Environmental Microbiology

Quantitative Analysis of O2 and Fe2+ Profiles in Gradient Tubes for Cultivation of Microaerophilic Iron(II)-Oxidizing Bacteria – U. Lueder – FEMS Microbiology Ecology

Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota – Lin-Xing Chen –  ISME Journal

Diversity patterns of microbial eukaryotes mirror those of bacteria in Antarctic cryoconite holes – Pacifica Sommers – FEMS Microbiology Ecology

Linking bacterial community structure to advection and environmental impact along a coast-fjord gradient of the Sognefjord, western Norway – Julia E.Storesund – Progress in Oceanography

Bacterial Succession on Sinking Particles in the Ocean’s Interior -Erik A. Pelve – Frontiers in Microbiology

Growth of Nitrosococcus-Related Ammonia Oxidizing Bacteria Coincides with Extremely Low pH Values in Wastewater with High Ammonia Content – Alexandra Fumasoli – Environmental Science & Technolology

Characteristics of Bacterial Communities in Cyanobacteria-Blooming Aquaculture Wastewater Influenced by the Phytoremediation with Water Hyacinth – Qing Zhou – Water

Biodegradation of phenol by cold-adapted bacteria from Antarctic soils – Gillian Li Yin Lee – Polar Biology

Built environment 

Bacterial community evolutions driven by organic matter and powder activated carbon in simultaneous anammox and denitrification (SAD) process – Cheng-Hao Ge – Bioresource Technology

Food microbiology

The Role of Oligosaccharides in Host-Microbial Interactions for Human Health –  Sarah Ross – Journal of Clinical Gastroenterology

Probiotics / prebiotics

An in vivo assessment of the cholesterol-lowering efficacy of Lactobacillus plantarum ECGC 13110402 in normal to mildly hypercholesterolaemic adults – Adele Costabile – PLOS One

Can Probiotics Reduce Diarrhea and Infant Mortality in Africa?: The Project of a Pilot Study – Mario Del Piano – Journal of Clinical Gastroenterology

Searching for the Perfect Homeostasis: Five Strains of Bifidobacterium longum From Centenarians Have a Similar Behavior in the Production of Cytokines –  Stefania Nicola – Journal of Clinical Gastroenterology

In Vitro Inhibition of Klebsiella pneumoniae by Lactobacillus delbrueckii Subsp. delbrueckii LDD01 (DSM 22106): An Innovative Strategy to Possibly Counteract Such Infections in Humans? – Luca Mogna – Journal of Clinical Gastroenterology

Protective Role of Postbiotic Mediators Secreted by Lactobacillus rhamnosus GG Versus Lipopolysaccharide-induced Damage in Human Colonic Smooth Muscle Cells –  Alessia Cicenia – Journal of Clinical Gastroenterology

In Vitro Activity of Lactobacillus fermentum LF5 Against Different Candida Species and Gardnerella vaginalis: A New Perspective to Approach Mixed Vaginal Infections? –  Francesca Deidda- Journal of Clinical Gastroenterology

Probiotics are a good choice in remission of inflammatory bowel diseases: A meta analysis and systematic review – Mahboube Ganji-Arjenaki – Journal of Cellular Physiology

Optimization of the quenching and extraction procedures for a metabolomic analysis of Lactobacillus plantarum – Qin Yang – Analytical Biochemistry

Phages and viruses

Internalization of a polysialic acid-binding Escherichia  colibacteriophage into eukaryotic neuroblastoma cells – Timo A. Leht – Nature Communication

The human respiratory virome after lung transplantation for COPD: A single centre, prospective, longitudinal study – A.B. Mitchell – Respiratory Medicine

Virome Capture Sequencing in Castleman Disease Identifies Associations with Herpesviridae Family Members but No Novel Viruses – Christopher Sheild Nabel – Blood

Bioinformatics

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation – Hyun Min Kang – Nature Biotechnology

CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences – Kristi Gdanetz – BMC Bioinformatics

Biotechnology

Engineered synthetic scaffolds for organizing proteins within the bacterial cytoplasm – Matthew J Lee – Nature Chemical Biology

Engineering chemical interactions in microbial communities – Douglas J. Kenny – Chemical Society Reviews

Cyclic lipopeptide signature as fingerprinting for the screening of halotolerant Bacillus strains towards microbial enhanced oil recovery – Bárbara C. S. Farias – Applied Microbiology and Biotechnology

Techniques

Low cost, low tech SNP genotyping tools for resource-limited areas: Plague in Madagascar as a model – Cedar L. Mitchell – PLOS Neglected Tropical Diseases

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation – John Beaulaurier – Nature Biotechnology

Microbes in the news 

Bacteria discovery in Antarctica prompts rethink of humanity’s search for alien life

When Lemur Families Cuddle, They Share Important Gut Bacteria

$3.9 million supports research to turn bacteria into biofuel producers

Bacteria and Art

Meet the Penn students using medical gauze and bacteria to create art for ‘speculative worlds’