Lots of papers on gut microbiota in today’s digest!

Multi-site human microbiome

The Female Urinary Microbiota/Microbiome: Clinical and Research Implications.

Brubaker L et al – Rambam Maimonides Med J

A case controlled study examining the bladder microbiome in women with Overactive Bladder (OAB) and healthy controls.
Curtiss N et al. – Eur J Obstet Gynecol Reprod Biol

Human respiratory microbiome

Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue.
Johnston D et al. – BMC Vet Res.

Human gut microbiome

The Gut Microbiota and the Hepatologist: Will Our Bugs Prove to be the Missing Link?

Pallen MJ and Quraishi MN – Digestive Diseases

A Specific Gut Microbiota Dysbiosis of Type 2 Diabetic Mice Induces GLP-1 Resistance through an Enteric NO-Dependent and Gut-Brain Axis Mechanism.

Grasset E et al – Cell Metab

Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease.

Loomba R et al  –  Cell Metab

16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome.

Almonacid DE – PLoS One

Autophagy Genes of Host Responds to Disruption of Gut Microbial Community by Antibiotics.

Singh SB – Dig Dis Sci

Interaction between the gut microbiome and mucosal immune system.

Shi N

Saccharomyces boulardii Administration Changes Gut Microbiota and Attenuates D-Galactosamine-Induced Liver Injury.
Yu L et al. – Sci Rep

Faecal microbiota transplantation for ulcerative colitis.
Drug Ther Bull.

Microbiome and colorectal cancer: Unraveling host-microbiota interactions in colitis-associated colorectal cancer development.
Kang M et al. Semin Immunol

Alpha-ketoglutarate (AKG) lowers body weight and affects intestinal innate immunity through influencing intestinal microbiota.
Chen S et al. – Oncotarget

The composition of gut microbiota in infant and its influencing factors
Liu W et al – Zhonghua Yu Fang Yi Xue Za Zhi

Occurrence of antibiotic resistance genes in the Faecal DNA of healthy omnivores, Ovo-Lacto vegetarians and vegans.
Milanović V et al. Mol Nutr Food Res

Seasonal variation in the copepod gut microbiome in the subtropical North Atlantic Ocean.
Shoemaker KM et al. Environ Microbiol

Models of antimicrobial pressure on intestinal bacteria of the treated host populations.
Volkova VV et al. – Epidemiol Infect

The food-gut human axis: the effects of diet on gut microbiota and metabolome.
De Angelis M et al.

The chicken or the egg dilemma: intestinal dysbiosis in multiple sclerosis.
Ochoa-Repáraz J, et al. – Ann Transl Med.

Impact of faecal microbiota transplantation on mouse digestive colonization with two extensively resistant bacteria.
Mahieu R et al – J Infect.

Plant, root, and soil microbiome

Lactic acid bacteria population dynamics during spontaneous fermentation of radish (Raphanus sativus L.) roots in brine.

Pardali E – World J Microbiol Biotechnol
Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Intraspecific Variation in the Skin-Associated Microbiome of a Terrestrial Salamander.

Prado-Irwin SR – Microb Ecol

Analysis of biofilm bacterial communities under different shear stresses using size-fractionated sediment.

Unraveling microbial structure and diversity of activated sludge in a full-scale simultaneous nitrogen and phosphorus removal plant using metagenomic sequencing.
Guo J et al – Enzyme Microb Technol.

The interacting roles of climate, soils, and plant production on soil microbial communities at a continental scale.
Waldrop MP et al. – Ecology

Correspondence of coral holobiont metabolome with symbiotic bacteria, archaea and Symbiodinium communities.
Sogin EM et al. – Environ Microbiol Rep
Fang H et al. Sci Rep.

Influence of root components of celery on pyrene bioaccessibility, soil enzymes and microbial communities in pyrene and pyrene-diesel spiked soils.
Wei J et al. – Sci Total Environ

Bioinformatics

ICoVeR – an interactive visualization tool for verification and refinement of metagenomic bins.
Broeksema B et al. – BMC Bioinformatics

Pregnancy and early life

Development of the cutaneous microbiome in the preterm infant: A prospective longitudinal study
Mohan Pammi et al. PLoS One

Human respiratory microbiome

The presence of bacterial microcolonies on the maxillary sinus ciliary epithelium in healthy young individuals
Monika Morawska-Kochman et al. PLoS One

Human gut microbiome

Review of mechanisms of deoxynivalenol-induced anorexia: The role of gut microbiota
Zhao Peng et al – JOURNAL OF APPLIED TOXICOLOGY

Probiotics are a good choice in remission of inflammatory bowel diseases: A meta analysis and systematic review
Mahboube Ganji-Arjenaki et al – JOURNAL OF CELLULAR PHYSIOLOGY

Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome.
Labus JS et al – Microbiome

The shrinking human gut microbiome.
Moeller AH. – Curr Opin Microbio

Animal experiments

Maternal obese-type gut microbiota differentially impact cognition, anxiety and compulsive behavior in male and female offspring in mice

Jing Chen et al. PLoS One

Dysbiosis of intestinal microbiota and decrease in paneth cell antimicrobial peptide level during acute necrotizing pancreatitis in rats
Annadora J. et al . PLoS One

Animal microbiome

Bacterial microbiome of the nose of healthy dogs and dogs with nasal disease
Barbara Tress, et al . PLoS One
Characterization of the fecal microbiome during neonatal and early pediatric development in puppies
Blake C. Guard et al. PLoS One

Effects of Saccharomyces cerevisiae fermentation products on dairy calves: Ruminal fermentation, gastrointestinal morphology, and microbial community.
Xiao JX et al – J Diary Sci

Studies on bacterial community composition are affected by the time and storage method of the rumen content
Yury Tatiana Granja-Salcedo et al. PLoS One

Competition drives the response of soil microbial diversity to increased grazing by vertebrate herbivores.
Eldridge DJ et al – Ecology

Diversity of culturable bacterial communities in the intestinal tracts of goldfish (Carassius auratus) and their ability to produce N-acyl homoserine lactone.
Sugita H et al – Folia Microbiol

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Crude oil impairs immune function and increases susceptibility to pathogenic bacteria in southern flounder
Keith M. Bayha et al. PLoS One

Pyrosequencing reveals microbial community dynamics in integrated simultaneous desulfurization and denitrification process at different influent nitrate concentrations.
Chen C et al – Chemosphere

Bioinformatics

Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses
Konstantin Yarygin et al. PLoS One

Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform
Chongqing Wen et al. PLoS One

The MB Digest Team hopes everyone had a good Labour Day holiday (or just a good day depending on where you are). Our Tuesday digest is full of fresh articles, a few news pieces, and lots going on in the Environmental Microbiome sections. Enjoy!

Events and jobs

PhD in soil microbiology
Teagasc Johnstown Castle

General microbiome

Analysis of stability to cheaters in models of antibiotic degrading microbial communities
András Szilágyi et al. – Journal of Theoretical Biology

Revew: Human genome-microbiome interaction: metagenomics frontiers for the aetiopathology of autoimmune diseases
Aycan Gundogdu & Ufuk Nalbantoglu – Microbial Genomics

Review: Fingerprinting microbiomes towards screening for microbial antibiotic resistance
Naifu Jin et al – Integrative Biology

Comparative genomics and metabolomics analyses of the adaptation mechanism in Ketogulonicigenium vulgare-Bacillus thuringiensis consortium
Nan Jia et al – Nature Scientific Reports

Multi-site human microbiome

Review: A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome
Maria Elisa Perez-Muñoz et al – Microbiome

Review: Interaction between the gut microbiome and mucosal immune system
Na Shi et al – Military Medical Research

Human gut microbiome

Bacterial Diversity of the Gastric Content of Preterm Infants during Their First Month of Life at the Hospital
Moles L. et al. – Frontiers in Nutrition

Opinion: The shrinking human gut microbiome
Moeller AH – Current Opinion in Microbiology

Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome
Labus JS et al. – Microbiome

Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes
Eliana Mariño et al. – Nature Immunology

Microbial diseases

The Novel ASIC2 Locus is Associated with Severe Gingival Inflammation
Zhang S. et al. – JDR Clinical & Translational Research

In vitro Multi-Species Biofilms of Methicillin-Resistant Staphylococcus aureus and Pseudomonas aeruginosa and Their Host Interaction during In vivo Colonization of an Otitis Media Rat Model
Yadav MK et al. – Frontiers in Cellular and Infectious Microbiology

Reduction in fecal microbiota diversity and short-chain fatty acid producers in Methicillin-resistant Staphylococcus aureus infected individuals as revealed by PacBio single molecule, real-time sequencing technology
J Zhao et al – European Journal of Clinical Microbiology & Infectious Diseases

Perspective: Treatable traits and therapeutic targets: goals for systems biology in infectious disease
Clark D. Russell & J. Kenneth Baillie – Current Opinion in Systems Biology

General Environmental Microbiome

Review: Effects and mechanisms of biochar-microbe interactions in soil improvement and pollution remediation: A review
Zhu X et al – Environmental Pollution

Sulfur flows and biosolids processing: Using Material Flux Analysis (MFA) principles at wastewater treatment plants
Fisher RM et al. – Journal of Environmental Management

Exploration of the relationship between biogas production and microbial community under high salinity conditions
Shaojie Wang et al – Nature Scientific Reports

Review: Phytoremediation of Water Bodies
E. Etim et al. – Current Environmental Engineering

Review: Role of Phytochelators in Land Reclamation: Recent Progress and Perspectives
Resham Sharma et al. – Current Environmental Engineering

Environmental Metabarcoding Reveals Contrasting Belowground and Aboveground Fungal Communities from Poplar at a Hg Phytomanagement Site
Alexis Durand et al. – Microbial Ecology

Monitoring global protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis under hypochlorite stress
Melanie Hillion et al – Nature Scientific Reports

A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes
Sarah L Grady et al – BMC Genomics

Interpreting Omic Data for Microbially Influenced Corrosion: Lessons from a Case Study Involving a Seawater Injection System
Craig Bartling et al – OnePetro

Land scale biogeography of arsenic biotransformation genes in estuarine wetland
Si-Yu Zhang et al – Environmental Microbiology

Animal experiments

Effects of Saccharomyces cerevisiae fermentation products on dairy calves: Ruminal fermentation, gastrointestinal morphology, and microbial community
Xiao JX et al. – Journal of Dairy Science

Immunological effects of reduced mucosal integrity in the early life of BALB/c mice
Bendtsen KM et al – PLoS One

Dietary Supplementation with Raspberry Whole Fruit Modifies the Relative Abundance of Fecal Microbial Communities in Obese Diabetic (db/db) Mice
Giuliana Noratto et al – The FASEB Journal

Chemical and pathogen-induced inflammation disrupt the murine intestinal microbiome
Mikayla A. Borton et al – Microbiome

Animal microbiome

Diversity of culturable bacterial communities in the intestinal tracts of goldfish (Carassius auratus) and their ability to produce N-acyl homoserine lactone
Haruo Sugita et al. – Folia Microbiologica

Viral gut metagenomics of sympatric wild and domestic canids, and monitoring of viruses: Insights from an endangered wolf population
Nádia Conceição-Neto et al – Ecology and Evolution

Characterization of the fecal microbiome during neonatal and early pediatric development in puppies
Blake C. Guard et al – PLoS One

The environmental and host-associated bacterial microbiota of Arctic seawater-farmed Atlantic salmon with ulcerative disorders
C Karlsen et al – Journal of Fish Diseases

Pre-print: Caterpillars lack a resident gut microbiome
Tobin J Hammer et al – bioRxiv

Bacterial microbiome of the nose of healthy dogs and dogs with nasal disease
Barbara Tress et al – PLoS One

Plant, root, and soil microbiome

First “charosphere” view towards the transport and transformation of Cd with addition of manure derived biochar
Wang L et al. – Environmental Pollution

Competition drives the response of soil microbial diversity to increased grazing by vertebrate herbivores
Eldridge DJ et al. – Ecology

Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content
Pankaj Trivedi et al – Environmental Microbiology

Altitudinal, seasonal and interannual shifts in microbial communities and chemical composition of soil organic matter in Alpine forest soils
José A. Siles et al – Soil Biology and Biochemistry

Water, estuarine and sediment microbiome

Pre-peer review: Microbiome succession during ammonification in eelgrass bed sediments
Cassandra L Ettinger et al – PeerJ

Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge
Cassandra L Ettinger et al – PeerJ

Extremophile and space microbiome

In-depth characterization of bacterial and archaeal communities present in the abandoned Kettara pyrrhotite mine tailings (Morocco)
Odile Bruneel et al – Extremophile
Microbial biotechnology

Impact of selectively enriched microbial communities on long-term fermentative biohydrogen production
Kanniah Goud R. et al – Bioresource Technology

Review: Cooperation in microbial communities and their biotechnological applications
Matteo Cavaliere et al – Environmental Microbiology

Metabolic engineering of Escherichia coli for higher alcohols production: An environmentally friendly alternative to fossil fuels
Ana L. Gonçalves & Manuel Simões – Renewable and Sustainable Energy Reviews

Weak magnetic field: A powerful strategy to enhance partial nitrification
Zhibin Wang et al – Water Research

General microbiology and evolution

Comparative genomics of host-symbiont and free-living Oceanobacillus species
Kumar Mondal A. et al – Genome Biology and Evolution

Draft Genome Sequence of Plantibacter flavus Strain 251 Isolated from a Plant Growing in a Chronically Hydrocarbon-Contaminated Site
Rhea Lumactud et al. – Genome Announcements

HexA is a versatile regulator involved in the control of phenotypic heterogeneity of Photorhabdus luminescens
Langer A. et al – PLoS One

Complete Genome Sequence of the Gamma-Aminobutyric Acid-Producing Strain Streptococcus thermophilus APC151
Daniel M Linares et al – Genome Announcements

Bioinformatics and statistics

MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data
Dhariwal A. et al – Nucleic Acids Research

Techniques and methods

Perspective: The Role of the Negative Control in Microbiome Analyses
Kyle Edmonds & Laura Williams – The FASEB Journal

Perspective: A Robust Framework for Microbial Archaeology
Warinner C. – Annual Review of Genomics and Human Genetics

Microbes in the news

Gut bacteria found to be linked to chronic fatigue syndrome
Victor Marchione – Belmarra Health News

Zapping bacteria with sanitizers made of paper
Phys.org

‘Electric’ bacteria can purify sewage water – fast
EuroNews

How The Gut May Influence Food Choices: Fruit Flies With More Bacteria Had Fewer Cravings
Janissa Delzo – Medical Daily

Harmless Bacteria on Teeth Can Hijack Harmful One That Causes Lung Infections, Study Finds
Magdalena Kegel – Cystic Fibrosis News

Retired US Navy Veteran Comments on Military Microbiome Study
Yahoo News

Microbes In Human Body: Connection Between Abundance Of Various Microbiota Species & Accessibility Of Its Resources
Piyali Roy – The Science Times

A review on how the human microbiome has changed from that of primates, plus articles on biofilm formation in soils, and the influence of microbiomes on bone and psychological health are just a few of the articles highlighted in todays Biks Picks!

Analysis of stability to cheaters in models of antibiotic degrading microbial communities – András Szilágyi – Journal of Theoretical Biology

Human vaginal microbiome

Vaginal ecosystem modeling of growth patterns of anaerobic bacteria in microaerophilic conditions – Audrie A. Medina-Colorado – Anaerobe

Human gut microbiome

Opinion: The shrinking human gut microbiome – Andrew H Moeller – Current Opinion in Microbiology

Review: Osteomicrobiology: The influence of gut microbiota on bone in health and disease – Rheinallt M. Jones – Bone

The Role of the Microbiome in Bipolar Disorder-A New Model – Robert Yolken – Biological Psychiatry

Gut Microbiome and Brain Functional Connectivity in Infants: A Preliminary Study Focusing on the Amygdala – Andrew Salzwedel – Biological Psychiatry

Gut Microbiota Distributions Predict Mood Disorder Symptoms and Mediate Dietary Interactions – Brittany Mason – Biological Psychiatry

Antimicrobial resistance in the Bacteroides fragilis group in faecal samples from patients receiving broad-spectrum antibiotics – Kia Cirkeline Møller Hansen – Anaerobe

Animal experiments

Impact of faecal microbiota transplantation on mouse digestive colonization with two extensively resistant bacteria – Rafael Mahieu – Journal of Infection

Changes of cecal microflora in chickens following Eimeria tenella challenge and regulating effect of coated sodium butyrate – Zuoyong Zhou – Experimental Parasitology

Plant, root, and soil microbiome

Preprint: Bacterial Biofilm Formation On Soil Fungi: A Widespread Ability Under Controls – Cora Miquel Guennoc – BioRxiv

Laboratory persistence in soil of thiacloprid, pendimethalin and fenarimol incubated with treated wastewater and dissolved organic matter solutions. Contribution of soil biota – José Antonio Rodríguez-Liébana – Chemosphere

Food microbiology

Effect of different marinating conditions on the evolution of spoilage microbiota and metabolomic profile of chicken breast fillets – Anastasia E. Lytou – Food Microbiology

Probiotics / prebiotics

A combination of the probiotic and prebiotic product can prevent the germination of Clostridium difficile spores and infection – M. Rätsep – Anaerobe

Gut microbiota-mediated pharmacokinetics of ginseng saponins – Dong-Hyun Kim – Journal of Ginseng Research

Microbes in the news

Rumblings of Parkinson’s: Gut Microbiome Shifts in Early Stage of Disease – ALZFORUM

Yersinia pestis, the plague bacteria, can survive inside Acanthamoeba for protection -OutBreakNewsToday