December 2, 2018

Highlights: Colonocyte metabolism shapes the gut microbiota, skin and gut microbiome of wild mammals, bacterial diversity in waterholes of Kruger National Park, Yeast diversity of glaciers, Laser MICROSAMPLING of soil community, origin & evolution of global RNA virome, Lymphoma virome dynamics, PUMA-for processing 16S rRNA taxonomy data  for analysis and visualization and many more.

General microbiome

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations – Raphael Eisenhofer – Trends in Microbiology

Review: Gut microbiota – our new important organ  – Rositsa Sandeva – Albanian Journal of Agricultural Sciences

Human gut microbiome

Altered gut microbiota after traumatic splenectomy is associated with endotoxemia – Hua Zhu – Emerging Microbes & Infections

Review: Colonocyte metabolism shapes the gut microbiota – Yael Litvak – Science

Gut Microbiota Modulates Interactions Between Polychlorinated Biphenyls and Bile Acid Homeostasis – Sunny Lihua Cheng – Toxilogical Sciences

Animal experiments 

An intensive milk replacer feeding program benefits immune response and intestinal microbiota of lambs during weaning – Qian Zhang – BMC Veterinary Research

Animal microbiome 

Bacterial diversity in the waterholes of the Kruger National Park: an eDNA metabarcoding approach – Maxwell J Farrell – Genome

Skin and gut microbiomes of a wild mammal respond to different environmental cues – Anton Lavrinienko – BMC Microbiome

Meta-Omics Tools in the World of Insect-Microorganism Interactions – Antonino Malacrinò – MDPI

Land Use Influences Antibiotic Resistance in the Microbiome of Soil Collembolans Orchesellides sinensis – Dong Zhu – Environmental Science and Technology

The equine gastrointestinal microbiome: Impacts of age and obesity – Philippa K. Morrison – Systems Microbiology

Changes in gut bacterial communities in canaries infected by Macrorhabdus ornithogaster – Patrizia Robino – Journal of Avian Pathology

Plant, root, and soil microbiome

Laser MICROSAMPLING of soil microbial community – M. V. Gorlenko – Journal of Biological Engineering

Poplar phyllosphere harbors disparate isoprene-degrading bacteria – Andrew T. Crombie – PNAS

Changes in litter quality induced by N deposition alter soil microbial communitiesYingbin Li – Soil Biology and Biochemistry

Analysis of Bacterial Communities in White Clover Seeds via High-Throughput Sequencing of 16S rRNA Gene – Wenna Gao – Current Microbiology

Impact of Bactrocera oleae on the fungal microbiota of ripe olive drupes – Ahmed Abdelfattah – PLoS One

Water and extremophile microbiome 

Preprint: Extent of the annual Gulf of Mexico hypoxic zone influences microbial community structure Lauren Gillies Campbell – bioRxiv

Review: Microbiologically influenced corrosion and current mitigation strategies: A state of the art review – Bhavya Kachiprath – Data in Brief

Habitat-specificity and diversity of culturable cold-adapted yeasts of a cold-based glacier in the Tianshan Mountains, northwestern China – Baolong Luo – Applied Microbiology and Biotechnology

Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal  – Aleksandra S. Zakharenko – Microbial Ecology

Phages and viruses

Origins and Evolution of the Global RNA Virome – Yuri I. Wolf – mBio

Lymphoma Virome Dynamics Revealed By Cell-Free DNA Sequencing – Joseph G Schroers-Martin – Blood

Techniques

Inner Workings: Mapping the microbiome location helps elucidate its role – Marcus Woo – PNAS

Preprint: FDA-ARGOS: A Public Quality-Controlled Genome Database Resource for Infectious Disease Sequencing Diagnostics and Regulatory Science Research – Heike Sichtig – bioRxiv

Preprint: PUMA: A tool for processing 16S rRNA taxonomy data for analysis and visualization – Keith Mitchell – bioRxiv

EMA-amplicon-based taxonomic characterisation of the viable bacterial community present in untreated and SODIS treated roof-harvested rainwater – André Strauss  -Environmental Science: Water Research & Technology

 

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November 30, 2018

Happy Friday! Today’s digest features the skin microbiome of lizards and frogs, bacterial changes during palm wine fermentation, and the impact of deforestation on soils in the Amazon.

General microbiome

Review: The microbiome in threatened species conservation – West – Biological Conservation

Human oral microbiome

Oxidative stress in the oral cavity is driven by individual-specific bacterial communities – Džunková – NPJ Biofilms and Microbiomes

Human gut microbiome

Alterations of the gut microbiome and plasma proteome in Chinese patients with adolescent idiopathic scoliosis – Shen – Bone

Animal experiments

Effect of gastric fluid aspiration on the lung microbiota of laboratory rats – Finn – Experimental Lung Research

Animal microbiome

Skin bacterial diversity is higher on lizards than sympatric frogs in tropical Australia – Weitzman – PeerJ

Impact of Bacillus spp. spores and gentamicin on the gastrointestinal microbiota of suckling and newly weaned piglets – Poulsen – PLoS One

Plant, root, and soil microbiome

Land Use Influences Antibiotic Resistance in the Microbiome of Soil Collembolans Orchesellides sinensis – Zhu – Environmental Science and Technology

Deforestation Impacts Network Co-occurrence Patterns of Microbial Communities in Amazon Soils – Khan – FEMS Microbiology Ecology

Review: VOCs-mediated hormonal signaling and crosstalk with plant growth promoting microbes – Tyagi – Critical Reviews in Biotechnology

Soil amendment alters soil physicochemical properties and bacterial community structure of a replanted apple orchard – Liang – Microbiological Research

Specialisation events of fungal metacommunities exposed to a persistent organic pollutant are suggestive of augmented pathogenic potential – Martins – Microbiome

Extemophile microbiome

Salino-alkaline lime of anthropogenic origin a reservoir of diverse microbial communities – Kalwasińska – Science of the Total Environment

Food microbiology

Preprint: Bacterial diversity and population dynamics during the fermentation of palm wine from Guerrero Mexico – Astudillo-Melgar – BioRxiv

Assessment of biogas production and microbial ecology in a high solid anaerobic digestion of major California food processing residues – Achmon – Bioresource Technology Reports

Science, publishing, and career

Preprint: Participation and Motivations of Grant Peer Reviewers: A Comprehensive Survey of the Biomedical Research Community – Gallo – BioRxiv

November 29, 2018

Today’s digest covers updates on human milk oligosaccharides, microbial life in cemetry, intestinal resistome, and benefits of intermittent fasting in human cohort and the gut microbiota in mice.

General microbiome
Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16–17, 2017 – Rashmi Sinha – Microbiome

Human gut microbiome

Human milk oligosaccharides, milk microbiome and infant gut microbiome modulate neonatal rotavirus infection – Sasirekha Ramani – Nature Communications

Interpersonal Variations in Gut Microbiota Profiles Supersedes the Effects of Differing Fecal Storage Conditions – Caspar Bundgaard-Nielsen – Scientific Reports

In-and-Out Molecular Changes Linked to the Type 2 Diabetes Remission after Bariatric Surgery: An Influence of Gut Microbes on Mitochondria Metabolism – Paulina Samczuk – International Journal of Molecular Sciences

Characterization of fungal dysbiosis in Japanese patients with inflammatory bowel disease – Takayuki Imai – Journal of Gastroenterology

Gut microbiota features of the geographically diverse Indian population – Sudarshan A. Shetty – BioRxiv

Animal experiments

Intermittent administration of a fasting-mimicking diet intervenes in diabetes progression, restores β cells and reconstructs gut microbiota in mice Siying Wei – Nutrition and Metabolism

Skin and gut microbiomes of a wild mammal respond to different environmental cues – Anton Lavrinienko – Microbiome

Mouse intestinal microbiota reduction favors local intestinal immunity triggered by antigens displayed in Bacillus subtilis biofilm – Cédric M. Vogt – Microbial Cell Factories

The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus – Alison Vrbanac – BMC Microbiology

Use of next generation sequencing to investigate the microbiota of experimentally induced wounds and the effect of bandaging in horses – Louis J. Kamus – PlosOne

Soil microbiome

Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments – Nina Dombrowski – Nature Communications

Built Environment

Microbial life beyond the grave: 16S rRNA gene-based metagenomic analysis of bacteria diversity and their functional profiles in cemetery environments – Akebe Luther King Abia – Science of the Total Environment

Techniques

Prediction of the intestinal resistome by a three-dimensional structure-based method – Etienne Ruppé – Nature Microbiology

Quantitative PCR provides a simple and accessible method for quantitative microbiome profiling – Ching Jian – BioRxiv

Microbes in the news

Poo found on every McDonald’s touchscreen tested – Metro

Non-microbiology picks

Effects of intermittent and continuous calorie restriction on body weight and metabolism over 50 wk: a randomized controlled trial – Ruth Schübel – The American Journal of Clinical Nutrition

 

November 28, 2018

Influence of bacterial biofilms from vats on cheese characteristics, the fecal virome of wild ducks, variation in fungal diversity associated with olive trees.

Pregnancy and early life

Review: Strategies for the Preservation, Restoration and Modulation of the Human Milk Microbiota. Implications for Human Milk Banks and Neonatal Intensive Care Units – Leónides Fernández – Frontiers in Microbiology

Human vaginal microbiome

Vaginal microbiome in pregnant women according to trimester and its association with preterm birth: critical appraisal of a cross-sectional study – Dimitrios Papoutsis – Obstetrics & Gynecology Science

Human gut microbiome

Microbial-Host Interactions in Inflammatory Bowel Disease, Functional Bowel Disease, Obesity and Obesity-Related Metabolic Disease – Shailja C Shah – Gastroenterology

Animal experiments

Bioactive Food Abates Metabolic and Synaptic Alterations by Modulation of Gut Microbiota in a Mouse Model of Alzheimer’s Disease – Tauqeerunnisa Syeda – Journal of Alzheimer’s Disease

Extract of the Microalga Nitzschia laevis Prevents High-Fat-Diet Induced Obesity in Mice by Modulating the Composition of Gut Microbiota – Bingbing Guo

Effects of Taste Signaling Protein Abolishment on Gut Inflammation in an Inflammatory Bowel Disease Mouse Model – Ya-Wen Du – Journal of Visualized Experiments

Animal microbiome

Use of next generation sequencing to investigate the microbiota of experimentally induced wounds and the effect of bandaging in horses – Louis J Kamus – PLOS ONE

Plant, root, and soil microbiome

The chirality of imazethapyr herbicide selectively affects the bacterial community in soybean field soil – Hao Wu – Environmental Science and Pollution Research

Genome‐Wide Association studies on the phyllosphere microbiome: embracing complexity in host‐microbe interactions – Kathleen Beilsmith – The Plant Journal

Invasive plants differentially affect soil biota through litter and rhizosphere pathways: a meta‐analysis – Pei Zhang – Ecology Letters

Analysis of the community composition and bacterial diversity of the rhizosphere microbiome across different plant taxa – Shaonan Lei – MicrobiologyOpen

Spatial and temporal variation of fungal endophytic richness and diversity associated to the phyllosphere of olive cultivars – Patrick Materatski – Fungal Biology

Water and extremophile microbiome

Pre-print: Metagenomic Insights Unveil the Dominance of Undescribed Actinobacteria in Pond Ecosystem of an Indian Shrine – Radhakrishnan Manikkam – bioRxiv

Built environment

A procedure for identifying chemical and biological risks for books in historic libraries based on microclimate analysis – Eva Schito – Journal of Cultural Heritage

Food microbiology

Influence of the early bacterial biofilms developed on vats made with seven wood types on PDO Vastedda della valle del Belìce cheese characteristics – Raimondo Gaglio – International Journal of Food Microbiology

Probiotics/prebiotics

Microbial consortia: promising probiotics as plant biostimulants for sustainable agriculture – Sheridan L Woo – Frontiers in Plant Science

Phages and viruses

Fecal virome composition of migratory wild duck species – Luis Alfonso Ramírez-Martínez – PLOS ONE

November 27, 2018

Microbial communities of IBS patients after fecal microbiota transplantation, the shipworm gill-associated microbiota, a profile of bioartist Ani Liu in our “bacteria art” section.

Human skin microbiome

The Microbiome in Atopic Dermatitis – Amy S Paller – The Journal of Allergy and Clinical Immunology

Human gut microbiome

Microbiome dynamics in obesity – Christoph A Thaiss – Science

The kinetics of gut microbial community composition in patients with irritable bowel syndrome following fecal microbiota transplantation – Tarek Mazzawi – PLOS ONE

Impact of Amoxicillin-Clavulanate followed by Autologous Fecal Microbiota Transplantation on Fecal Microbiome Structure and Metabolic Potential – Christopher Bulow – mSphere

Comparison of the gut microbiota of obese individuals from different geographic origins – Emmanouil Angelakis – New Microbes and New Infections

Review: Fire in the Forest: Adverse Effects of Antibiotics on the Healthy Human Gut Microbiome – Manosha Perera – International Journal of Medical Reviews

Animal experiments

Proteomic Analysis of Microbial Induced Redox-Dependent Intestinal Signaling – Jason D Matthews – Redox Biology

Population and Culture Age Influence the Microbiome Profiles of House Dust Mites – Jan Hubert – Microbial Ecology

Animal microbiome

Symbiotic microbes affect the expression of male reproductive genes in Glossina m. morsitans – Francesca Scolari – BMC Microbiology

The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei – Thais L Brito – PLOS ONE

Plant, root, and soil microbiome

Host-specific signatures of the cell wall changes induced by the plant parasitic nematode, Meloidogyne incognita – Refik Bozbuga – Scientific Reports

The effects of struvite and sewage sludge on plant yield and the microbial community of a semiarid Mediterranean soil – F Bastida – Geoderma

Review: Effects of elevated carbon dioxide on environmental microbes and its mechanisms: A review – Tong Yu – Science of the Total Environment

Water and extremophile microbiome

Combining fish and benthic communities into multiple regimes reveals complex reef dynamics – Mary K Donovan – Scientific Reports

Diversity and predictive metabolic pathways of the prokaryotic microbial community along a groundwater salinity gradient of the Pearl River Delta, China – Shilei Sang – Scientific Reports

Bioinformatics

Pre-print: Naught all zeros in sequence count data are the same – Justin D Silverman – bioRxiv

Microbes in the news

A bacterium’s enemy isn’t your friend – Michael S. Gilmore – Nature

Bacteria art

Portrait of the Artist as a Microbial Growth – Kevin Litman-Navarro – The Outline

November 16, 2018

Happy Friday! Today’s digest includes the effects of chewing gum on the oral microbiome, the gill microbiome of mangrove shipworms, and the rumen microbiome of dairy cows. Enjoy!

Human oral microbiome

Effects of xylitol-containing chewing gum on the oral microbiota – Takeuchi – Journal of Oral Science

Human gut microbiome

Gut microbiome transition across a lifestyle gradient in Himalaya – Jha – PLoS Biology

Fecal chromogranins and secretogranins are linked to the fecal and mucosal intestinal bacterial composition of IBS patients and healthy subjects – Sundin – Scientific Reports

Animal experiments

Specific Members of the Gut Microbiota are Reliable Biomarkers of Irradiation Intensity and Lethality in Large Animal Models of Human Health – Carbonero – Radiation Research

Gut microbiota development in mice is affected by hydrogen peroxide produced from amino acid metabolism during lactation – Shigeno – FASEB Journal

Commensal bacteria contribute to insulin resistance in aging by activating innate B1a cells – Bodogai – Science Translational Medicine

Estrogen-mediated gut microbiome alterations influence sexual dimorphism in metabolic syndrome in mice – Kaliannan – Microbiome

Effects of Intraoperative Vagal Nerve Stimulation on the Gastrointestinal Microbiome in a Mouse Model of Amyotrophic Lateral Sclerosis – Haney – Comparative Medicine

Animal microbiome

Assessing the Microbiota of Black Soldier Fly Larvae (Hermetia illucens) Reared on Organic Waste Streams on Four Different Locations at Laboratory and Large Scale – Wynants – Microbial Ecology

The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei – Brito – PLoS One

Illumina sequencing analysis of the ruminal microbiota in high-yield and low-yield lactating dairy cows – Tong – PLoS One

Plant, root, and soil microbiome

Rootstocks shape the rhizobiome: Rhizosphere and endosphere bacterial communities in the grafted tomato system – Poudel – Applied and Environmental Microbiology

Water and extremophile microbiome

Aquatic ecotoxicity of an antidepressant, sertraline hydrochloride, on microbial communities – Yang – Science of The Total Environment

Probing the ecological and evolutionary history of a thermophilic cyanobacterial population via statistical properties of its microdiversity – Rosen – PLoS One

Built environment

Activated sludge bacterial communities of typical wastewater treatment plants: distinct genera identification and metabolic potential differential analysis – Zhang – AMB Express

Analysis of bacteria stress responses to contaminants derived from shale energy extraction – Santos – Environmental Science: Processes & Impacts

Probiotics/prebiotics

Gut microbiota of preterm infants supplemented with probiotics: sub-study of the ProPrems trial – Plummer – BMC Microbiology

November 14, 2018

Today’s digest is about how dietary shifts and low gluten diet changes the intestinal microbiome, fecal microbiota transplant in intestinal disorders, characterization of the most abundant bacteriophage family in the human gut, and Raman spectroscopy based method for fast identification of antibiotic resistance bugs.

Human gut microbiome

Fecal microbiota transplantation for refractory immune checkpoint inhibitor-associated colitis – Yinghong Wang – Nature Medicine

A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults – Lea BS Hansen – Nature Communications

Resilience of human gut microbial communities for the long stay with multiple dietary shifts – Hong Liu – Gut

Microbiome and its relation to gestational diabetes – Ramon V. Cortez – Endocrine

Effect of bifidobacterium breve A-1 on anxiety and depressive symptoms in schizophrenia: A proof-of-concept study – Ryo Okubo – Journal of Affective Disorders

Fecal Akkermansia muciniphila Is Associated with Body Composition and Microbiota Diversity in Overweight and Obese Women with Breast Cancer Participating in a Presurgical Weight Loss Trial – Andrew D Fruge – Journal of the Academy of Nutrition and Dietetics

An Open-Labeled Study on Fecal Microbiota Transfer in Irritable Bowel Syndrome Patients Reveals Improvement in Abdominal Pain Associated with the Relative Abundance of Akkermansia Muciniphila – Cruz-Aguliar RM – Digestion

Animal experiments

Berberine alleviates insulin resistance by reducing peripheral branched-chain amino acids – Shi-Jun Yue – American Journal of Physiology Endocrinology and Metabolism

Air microbiome

A long-term survey unveils strong seasonal patterns in the airborne microbiome coupled to general and regional atmospheric circulations – Joan Cáliz – PNAS

Phages and viruses

ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis – Andrey N Shkoporov – Nature Communications

Techniques

Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples – Yuan Gao – Nature Methods

Dynamic linear models guide design and analysis of microbiota studies within artificial human guts – Justin D Silverman – Microbiome

Microbes in the news

Chinese scientists develop novel instrument for rapid profiling of antimicrobial resistance – EurekaAlert

Microbes on the market

Chr. Hansen Receives Joint Innovation Fund Grant to Develop Next Generation Microbial Solutions for Agriculture – Microbiome times

Non-microbiology picks

Remission of Human Type 2 Diabetes Requires Decrease in Liver and Pancreas Fat Content but Is Dependent upon Capacity for β Cell Recovery – Roy Taylor – Cell Metabolism