September 18, 2018

Quite a few articles of interest today:

  1. Foods that are protective of the gut microbiome: Specific oligosaccharides in breast milk can compensate for the effects of C-section births, and cranberries can compensate for the effects of dietary changes in mice.
  2. A possible bi-directional relationship between the gut microbiome and high altitudes: Specific differences in the gut microbiome are associated with differences in tolerance to high altitudes in males, and exposure to high altitudes can alter the gut microbiome in mice.
  3. Microbes in Space: Nitrogen cycle nicroorganisms that may be able to produce food, water and O2 in space, and exposing desert extremophiles to Martian conditions to learn about the kinds of bacteria on other planets

Also: How smoking impacts the lung virome, the association between fecal microbiome profile and phylogeny in deer genera, and the development of the dust microbiome over time in a classroom

Pregnancy and early life

*Fucosylated oligosaccharides in mother’s milk alleviate the effects of caesarean birth on infant gut microbiota – Katri Korpela – Scientific Reports

The influence of maternal vaginal flora on the intestinal colonization in newborns and 3-month-old infants – Iwona Gabriel – The Journal of Maternal-Fetal & Neonatal Medicine

Fecal Volatile Organic Compounds in Preterm Infants Are Influenced by Enteral Feeding Composition – Sofia el Manouni el Hassani – Sensors

Multi-site human microbiome

Review: Talk to your gut: the oral-gut microbiome axis and its immunomodulatory role in the etiology of rheumatoid arthritis – Marines du Teil Espina – FEMS Microbiology Reviews

Human respiratory microbiome

*Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome – Ann C. Gregory – Respiratory Research

Human anal microbiome

Anal microbial patterns and oncogenic HPV in a pilot study of Nigerian men who have sex with men at risk for or living with HIV – Rebecca G Nowak – AIDS Research and Human Retroviruses

Human gut microbiome

*Associations between the gut microbiota and host responses to high altitude – J. Philip Karl – American Journal of Physiology

Intestinal barrier integrity in patients with plaque psoriasis – Mariusz Sikora – The Journal of Dermatology

Review: Mechanisms by which gut microorganisms influence food sensitivities
– Alberto Caminero – Nature Reviews Gastroenterology & Hepatology

Review: Selective sensitivity of the gut microbiome to iron chelators in polybacterial abdominal sepsis – Kayle Dickson – Medical Hypotheses

Review: ADHD-originating in the gut? The emergence of a new explanatory model – Anna M. Sandgren – Medical Hypotheses

Review: Guideline for the Management of Clostridium Difficile Infection in Children and Adolescents With Cancer and Pediatric Hematopoietic Stem-Cell Transplantation Recipients – Caroline Diorio – Journal of Clinical Oncology

Review: Altered Gut Microbiota in Type 2 Diabetes: Just a Coincidence? – Antonio Sircana – Current Diabetes Reports

Review: Bowel Biofilms: Tipping Points between a Healthy and Compromised Gut? – Hanne L.P. Tytgat – Trends in Microbiology

Review: Fecal microbiota transplant – a new frontier in inflammatory bowel disease – Sunkara T – Dove Press

Review: Gut microbiota, cognitive frailty and dementia in older individuals: a systematic review –  Ticinesi A – Dove Press

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Animal experiments

Deletion of poly(ADP‑ribose) polymerase-1 changes the composition of the microbiome in the gut – András Vida – Molecular Medicine Reports

Lactobacillus reuteri F‐9‐35 Prevents DSS‐Induced Colitis by Inhibiting Proinflammatory Gene Expression and Restoring the Gut Microbiota in Mice – Mao‐cheng Sun – Journal of Food Science

*Cranberries attenuate animal-based diet-induced changes in microbiota composition and functionality: A randomized crossover controlled feeding trial – Jose Rodríguez-Morató – The Journal of Nutritional Biochemistry

*The effect of exposure to high altitude and low oxygen on intestinal microbial communities in mice – Wei Zhang – PLOS ONE

The Effects of Berberine on the Gut Microbiota in Apc min/+ Mice Fed with a High Fat Diet – Huan Wang – Molecules

The influence of gut microbiota dysbiosis to the efficacy of 5-Fluorouracil treatment on colorectal cancer – Lu Yuan – Biomedicine & Pharmacotherapy

Protein deficiency reduces efficacy of oral attenuated human rotavirus vaccine in a human infant fecal microbiota transplanted gnotobiotic pig model – Ayako Miyazaki – Vaccine

In vitro experiments

Butyrate upregulates the TLR4 expression and the phosphorylation of MAPKs and NK‑κB in colon cancer cell in vitro – Tengfei Xiao – Oncology Letters

Animal microbiome

Comparison of the gut microbiota of captive common bottlenose dolphins, Tursiops truncatus in three aquaria – Akihiko Suzuki – Journal of Applied Microbiology

Bacteria richness and antibiotic-resistance in bats from a protected area in the Atlantic Forest of Southeastern Brazil – Vinícius C. Cláudio – PLOS ONE

*Divergence of Fecal Microbiota and Their Associations With Host Phylogeny in Cervinae – Jiaying Li – Frontiers in Microbiology

Probiotics modify body weight together with anxiety states via pro-inflammatory factors in HFD-treated Syrian golden hamster – Ennio Avolio – Behavioural Brain Research

Effects of short-term fasting on in vivo rumen microbiota and in vitro rumen fermentation characteristics – Jong Nam Kim – Asian-Australas Journal of Animal Sciences

The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency – Chloe Matthews – Gut

MicrobesEvaluation of conjunctival microbiota in clinically normal persian squirrels (Sciurus Anomalus) – Houman Faghihi – Journal of Zoo and Wildlife Medicine

Plant, root, and soil microbiome

Trichoderma gamsii affected herbivore feeding behaviour on Arabidopsis thaliana by modifying the leaf metabolome and phytohormones – Dongmei Zhou – Microbial Biotechnology

Responses of soil biological traits and bacterial communities to nitrogen fertilization mediate maize yields across three soil types – Hailing Yu – Soil and Tillage Research

Soil microbial response to Rhododendron understory removal in southern Appalachian forests: Effects on extracellular enzymes – Ernest D. Osburn – Soil Biology and Biochemistry

Insight into Bacterial Community Diversity and Monthly Fluctuations of Medicago sativa Rhizosphere Soil in Response to Hydrogen Gas Using Illumina High-Throughput Sequencing – Zhiying Li – Current Microbiology

Bacterial diversity in rhizosphere of Paspalum scrobiculatum L. (kodo millet) is revealed with shotgun metagenome sequencing and data analysis – Ratna Prabha – Data in Brief

Responses of soil biological traits and bacterial communities to nitrogen fertilization mediate maize yields across three soil types – Hailing Yu – Soil and Tillage Research

Microbial Ecology

Effects of Cd, Cu, Zn and their combined action on microbial biomass and bacterial community structure – Jiuwei Song – Environmental Pollution

Effects of graphene oxides and silver-graphene oxides on aquatic microbial activity – Kwanyoung Ko – Science of The Total Environment

Built environment

*Longitudinal development of the dust microbiome in a newly opened Norwegian kindergarten – Anders B. Nygaard – Microbiome

Microbiological analysis of contact lens cases: impact of the hospital environment – Vinicius Targa Villas Bôas – Arquivos Brasileiros de Oftalmologia

Microbes in space

*Nitrogen cycle microorganisms can be reactivated after Space exposure – Ralph E. F. Lindeboom – Scientific Reports

*Desert cyanobacteria under space and planetary simulations: a tool for searching for life beyond Earth and supporting human space exploration – Daniela Billi – International Journal of Astrobiology

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Bioinformatics

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis – Gherman V. Uritskiy – Microbiome

Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations  – Alex N Salazar – Bioinformatics

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Microbes in the news

The electrifying energy of gut microbes – Laty A. Cahoon – Nature News and Views

Bacteria and Art

How Anicka Yi’s Science Experiments Are Expanding the Boundaries of Art – Andrew Russeth – W

 

 

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September 17, 2018

In today’s Microbiome Digest, look for rhizobacteria that affect plant size, methanogenesis in salt marsh sediments, a murine model for periodontitis, and an exciting preprint that identifies a microbiome in dinosaur bones! Plus, as bonus non-microbiology topics, we consider authorship norms across different disciplines and how forensics might work on Mars.

General Microbiome
(preprint) Life Inside A Dinosaur Bone: A Thriving Microbiome – Evan Thomas Saitta – bioRxiv

Metabolic Interactions of a Chain Elongation Microbiome – Wenhao Han – Applied and Environmental Microbiology

Human Gut Microbiome
Passing the “Acid Test”: Do Proton Pump Inhibitors Affect the Composition of the Microbiome? – Tien Dong – Digestive Diseases and Sciences

The gastric mucosal-associated microbiome in patients with gastric polyposis – Rongrong Ren – Scientific Reports

Animal Experiments
An experimental murine model to study periodontitis – Julie Marchesan – Nature Protocols

The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice – Alida Kindt – Nature Communications

Animal Microbiome
Global Networks of Symbiodinium-Bacteria Within the Coral Holobiont – Rachele Bernasconi – Microbial Ecology

(preprint) Gut microbial compositions mirror caste-specific diets in a major lineage of eusocial insects – Saria Otani -bioRxiv

Plant, Root, and Soil Microbiome
Plant growth-promoting rhizobacteria promote plant size inequality – Alan C. Gange – Scientific Reports

Diversity of active viral infections within the Sphagnum microbiome – Joshua MA Stough – Applied and Environmental Microbiology

The impact of high throughput sequencing on plant health diagnosticsThe impact of high throughput sequencing on plant health diagnostics – Ian Adams -European Journal of Plant Pathology

Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment – Eleanor Jameson – ISME Journal

Water and Extremophile Microbiome
Living at the frontiers of life: extremophiles in Chile and their potential for bioremediation – Roberto Orellana – Frontiers in Microbiology

Spatial structuring of bacterial communities in epilithic biofilms in the Acquarossa river (Italy) – Carolina Chiellini – FEMS Microbial Ecology

Bioinformatics
A small‐sample kernel association test for correlated data with application to microbiome association studies – Xiang Zhan – Genetic Epidemiology

Science, Publishing, and Career
Thousands of scientists publish a paper every five days – John P. A. Ioannidis – Nature

Alyson’s Non-Microbiology Picks
Sensing with tools extends somatosensory processing beyond the body – Luke E. Miller- Nature

How Will Police Solve Murders on Mars? – Geoff Manaugh – The Atlantic

September 16, 2018

Good morning! the publications from today’s microbiome digest covering the followings: Tick Microbiome, Chronic fatigue syndrome and alteration in the oral microbiome, CRC associated metabolites quantified from the faecal extracts, vaginal microbiome during cytolytic vaginosis, rumen and fecal bacterial community in high-production dairy cattle, and estimation of the expected variation in microbiome measurements (methodological research). Enjoy reading.

General microbiome

Thesis: Investigating the effects of the gut-associated microbial community on the growth of the eastern spruce budworm – Melbert Schwarz – Thesis

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing – Lisa Couper – Journal of Visualized Experiments: JoVE

Alcohol consumption increase susceptibility to pneumococcal pneumonia in a humanized murine HIV model mediated by intestinal dysbiosis – Derrick R.Samuelson – Alcohol 

Oral microbiome

Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function – Taiwu Wang – PLOSONE

Human gut microbiome

Metabolite quantification of faecal extracts from colorectal cancer patients and healthy controls – Gwénaëlle Le Gall – Oncotarget

Vaginal microbiome

Characterization of the vaginal microbiome during cytolytic vaginosis using high-throughput sequencing – Haihong Xu – Wiley

Animal microbiome

High-production dairy cattle exhibit different rumen and fecal bacterial community and rumen metabolite profile than low-production cattle – Yingyu Mu – MicrobiologyOpen

Characterization of the Functional Changes in Mouse Gut Microbiome Associated with Increased Akkermansia muciniphila Population Modulated by Dietary Black Raspberries – Pengcheng Tu – ACS Omega

Plant, root, and soil microbiome

Dynamics of soil respiration and microbial communities: Interactive controls of temperature and substrate quality – Rana ShahbazAli – Soil Biology and Biochemistry

Microbial community structure and functions differ between native and novel (exotic-dominated) grassland ecosystems in an 8-year experiment – Aleksandra Checinska Sielaff – Plant and Soil

Impacts of heavy metals and soil properties at a Nigerian e-waste site on soil microbial community – Bo Jiang – Journal of Hazardous Material

Insight into Bacterial Community Diversity and Monthly Fluctuations of Medicago sativa Rhizosphere Soil in Response to Hydrogen Gas Using Illumina High-Throughput Sequencing – Zhiying Li – Current Microbiology

Extreme environmental microbiome

Bacterial diversity in snow from mid-latitude mountain areas: Alps, Eastern Anatolia, Karakoram and Himalaya – Roberto Sergio AZZONI – Annals of Glaciology

Water and extremophile microbiome

Characterization of bacterial and microbial eukaryotic communities associated with an ephemeral hypoxia event in Taihu Lake, a shallow eutrophic Chinese lake – Jian Cai – Environmental Science and Pollution Research

Inherent bacterial community response to multiple heavy metals in sediment from river-lake systems in the Poyang Lake, China – Hua Zhang – Ecotoxicology and Environmental Safety

Bioinformatics

Machine learning analysis of microbial flow cytometry data from nanoparticles, antibiotics and carbon sources perturbed anaerobic microbiomes – Abhishek S. Dhoble – Journal of Biological Engineering

Techniques

Methodology: Quantification of variation and the impact of biomass in targeted 16S rRNA gene sequencing studies – Jeffrey M. Bender – Microbiome

September 15, 2018

Have a nice weekend! Today, we have several papers, covering different aspects of the microbiome! Some highlights (in bold): the role of microbiota in cancer immunotherapy success; interesting study about the lung microbiota and smoking; changes in gut microbiota in asthma patients, microbiota changes in high-salt feces; an interesting article about the potential effect of dogs in veteran rehabilitation; a review about periodontitis and the microbiome; a ecophylogenetic study about mammalian microbiome, and more!

 

Human and General Microbiome

Metagenomic Approaches for Understanding New Concepts in Microbial Science – Luana de Fátima Alves – International Journal of Genomics

Review: Epigenetic Mechanisms Link Maternal Diets and Gut Microbiome to Obesity in the Offspring – Yuanyuan Li – Frontiers in Genetics

Review: NLRP3 inflammasome in colitis and colitis-associated colorectal cancer – Agampodi Promoda Perera – Mammalian Genome

Oral Microbiome Shifts From Caries-Free to Caries-Affected Status in 3-Year-Old Chinese Children: A Longitudinal Study – He Xu – Frontiers in Microbiology

Review: Roles of intestinal microbiota in response to cancer immunotherapy – Jing Cong – European Journal of Clinical Microbiology & Infectious Diseases

Intestinal dysbiosis and hormonal neuroendocrine secretion in the fibromyalgic patient: Relationship and correlations – Giovanni Tomasello – Biomedical Papers

Macroecology to Unite All Life, Large and Small – Ashley Shade – Trends in Ecology and Evolution

Dichotomous development of the gut microbiome in preterm infants – Thao T. B. Ho – Microbiome

Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome – Ann C. Gregory – Respiratory Research

A metagenome-wide association study of gut microbiota in asthma in UK adults – Qi Wang – BMC Microbiology

The Cutaneous Microbiome and Wounds: New Molecular Targets to Promote Wound Healing – Taylor R. Johnson – International Journal of Molecular Sciences

Phthalate Exposure and Odds of Bacterial Vaginosis Among U.S. Reproductive-Aged Women, NHANES 2001-2004 – Ruth J.Geller – Reproductive Toxicology

Para-cresol production by Clostridium difficile affects microbial diversity and membrane integrity of Gram-negative bacteria – Ian J. Passmore – PLoS Pathogens

Salt in stools is associated with obesity, gut halophilic microbiota and Akkermansia muciniphila depletion in humans – E. H. Seck – International Journal of Obesity

The local microbiome after pediatric bladder augmentation: intestinal segments and the native urinary bladder host similar mucosal microbiota – Z.F. Kispal – Journal of Pediatric Urology

The Gut-Brain Axis in Alzheimer’s Disease and Omega-3. A Critical Overview of Clinical Trials – Francesca La Rosa – Nutrients

Associations between Flavonoid Intakes and Gut Microbiota in a Group of Adults with Cystic Fibrosis – Li Li – Nutrients

Review: Insights into the Human Virome Using CRISPR Spacers from Microbiomes – Claudio Hidalgo-Cantabrana – Viruses

Review: Probiotics in the Treatment of Colorectal Cancer –  Robert Hendler – Medicines

Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease – Shu Mei Teo – Cell Host and Microbe

Human skin volatiles: Passive sampling and GC × GC-ToFMS analysis as a tool to investigate the skin microbiome and interactions with anthropophilic mosquito disease vectors – Alexis P. Roodt – Journal of Chromatography B

Commentary: Regulating stool for microbiota transplantation – Pilar N. Ossorio – Gut Microbes

Associations between the gut microbiota and host responses to high altitude – J. Philip Karl – Gastrointestinal and Liver Physiology

Exploring service dogs for rehabilitation of veterans with PTSD: A microbiome perspective – Andrew J.,Billera Hoisington – Rehabilitation Psychology

Mucosal associated invariant T cells from human breast ducts mediate a Th17-skewed response to bacterially exposed breast carcinoma cells – Nicholas A. Zumwalde – Breast Cancer Research

Periodontitis and the microbiome: a systematic review and meta-analysis – Fabrizio Guerra – Minerva Stomatologica

Formal Comment: The microbiome and the human: A reply to Parke and colleagues – Tobias Rees – PLoS Biology

Microbiota-gut-brain research: a critical analysis – Katarzyna B. Hooks – Behavioral and Brain Sciences

 

Animal Microbiome

Ecophylogenetics Clarifies the Evolutionary Association between Mammals and Their Gut Microbiota – Christopher A. Gaulke – mBio

The Inhibitory Innate Immune Sensor NLRP12 Maintains a Threshold against Obesity by Regulating Gut Microbiota Homeostasis – Agnieszka D. Truax – Cell Host and Microbe

American ginseng microbial metabolites attenuate DSS-induced colitis and abdominal pain – Chong-Zhi Wang – International Immunopharmacology

Impact of violacein from Chromobacterium violaceum on the mammalian gut microbiome – Heidi Pauer – PLoS ONE

Bacterial community composition in the salivary glands of triatomines (Hemiptera: Reduviidae) – Michele Souza Lima – PLoS Neglected Tropical Diseases

Postnatal Administration of Lactobacillus rhamnosus HN001 Ameliorates Perinatal Broad-Spectrum Antibiotic-Induced Reduction in Myelopoiesis and T cell Activation in Mouse Pups – Eva Fuglsang – Molecular Nutrition and Food Research

Absorption of Codonopsis pilosula Saponins by Coexisting Polysaccharides Alleviates Gut Microbial Dysbiosis with Dextran Sulfate Sodium-Induced Colitis in Model Mice – Yaping Jing – BioMed Research International

Tributyrin Supplementation Protects Immune Responses and Vasculature and Reduces Oxidative Stress in the Proximal Colon of Mice Exposed to Chronic-Binge Ethanol Feeding – B. Glueck – Journal of Immunology Research

Fecal Hyodeoxycholic Acid Is Correlated With Tylosin-Induced Microbiome Changes in Growing Pigs – Michaela P. Trudeau – Frontiers in Veterinary Science

Yeast Probiotics Shape the Gut Microbiome and Improve the Health of Early-Weaned Piglets – Jinqiang Xu – Frontiers in Microbiology

Probiotic Bacillus amyloliquefaciens C-1 Improves Growth Performance, Stimulates GH/IGF-1, and Regulates the Gut Microbiota of Growth-Retarded Beef Calves – Renjia Du – Frontiers in Microbiology

The Microbiome of the Gastrointestinal Tract of a Range-Shifting Marine Herbivorous Fish – Jacquelyn Jones – Frontiers in Microbiology

Intestinal Microbiome-Metabolome Responses to Essential Oils in Piglets – Yuan Li – Frontiers in Microbiology

Review: Managing the Microbial Community of Marine Fish Larvae: A Holistic Perspective for Larviculture – Olav Vadstein – Frontiers in Microbiology

Functional modulation of caecal fermentation and microbiota in rat by feeding bean husk as a dietary fibre supplement – H. Myint – Beneficial Microbes

Effects of short-term fasting on in vivo rumen microbiota and in vitro rumen fermentation characteristics – Jong Nam Kim – Asian-Australian Journal of Animal Sciences

The effect of exposure to high altitude and low oxygen on intestinal microbial communities in mice – Wei Zhang – PLoS ONE

 

Food Microbiome

Lactic Acid Bacterium Population Dynamics in Artisan Sourdoughs Over One Year of Daily Propagations Is Mainly Driven by Flour Microbiota and Nutrients – Fabio Minervini – Frontiers in Microbiology

Effect of Pressure, Reconstituted RTE Meat Microbiota, and Antimicrobials on Survival and Post-pressure Growth of Listeria monocytogenes on Ham – Januana S. Teixeira – Frontiers in Microbiology

 

Plant Microbiome

G3 PhyloChip Analysis Confirms the Promise of Plant-Based Culture Media for Unlocking the Composition and Diversity of the Maize Root Microbiome and for Recovering Unculturable Candidate Divisions/Phyla – Mohamed S. Sarhan – Microbes and Environments

Root exudates drive the soil-borne legacy of aboveground pathogen infection – Jun Yuan – Microbiome

Review: Mycorrhizal microbiomes – Mika T. Tarkka – Mycorrhiza

 

Bioinformatics

GePMI: A statistical model for personal intestinal microbiome identification – Zicheng Wang – npj Biofilms and Microbiomes

Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes – Suzanne M. Kosina – BMC Microbiology

 

Other

Temporal variability and stability of the fecal microbiome: the Multiethnic Cohort Study – Benjamin C Fu – Cancer Epidemiology, Biomarkers & Prevention

A flavin-based extracellular electron transfer mechanism in diverse Gram-positive bacteria – Samuel H. Light – Nature

 

12 September​​ 2018

Today’s digest is full of exciting microbiome reviews and new techniques for analysing microbiome datasets.

General Microbiome

Complete genome sequence of Bifidobacterium choerinum FMB-1, a resistant starch-degrading bacterium.Jung DH. Journal of Biotechnology

Gut Microbiome

REVIEW: Nutritional Modulation of Innate Immunity: The Fat-Bile-Gut Connection.Chevre R. Trends in Endocrinology and Metabolism

Plant, Soil, and Water Microbiome

Microbial composition, potential functional roles and genetic novelty in gypsum-rich and hypersaline soils of Monegros and Gallocanta (Spain). Menéndez-Serra M.Science of the Total Environment

Combined polyhydroxyalkanoates (PHA) and 1,3-propanediol production from crude glycerol: Selective conversion of volatile fatty acids into PHA by mixed microbial consortia.Burniol-Figols A. Water Research

Quantification of Agrobacterium vitis from Grapevine Nursery Stock and Vineyard Soil using Droplet Digital PCR.Voegel TM. Plant Disease

Below-ground-above-ground Plant-microbial Interactions: Focusing on Soybean, Rhizobacteria and Mycorrhizal Fungi. Igiehon NO. The Open Microbiology Journal

Animal Experiments and Microbiome

Effects of exogenous microbial inoculum on the structure and dynamics of bacterial communities in swine carcass composting. Yang X. Canadian Journal of Microbiology

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing.Couper L. Journal of Visualized Experiments

Effects of dietary lysozyme levels on growth performance, intestinal morphology, immunity response and microbiota community of growing pigs. Zou L. Journal of the Science of Food and Agriculture

REVIEW: A Review of the Effect of Management Practices on <i>Campylobacter</i> Prevalence in Poultry Farms.Sibanda N. Frontiers in Microbiology.

Metabolic Syndrome During Perinatal Period in Sows and the Link With Gut Microbiota and Metabolites. Cheng C. Frontiers in Microbiology

Fecal Microbiota Transplantation Ameliorates Experimentally Induced Colitis in Mice by Upregulating AhR. Wei YL. Frontiers in Microbiology

Prebiotics and Probiotics

Probiotic <i>Lactobacillus plantarum</i> Promotes Intestinal Barrier Function by Strengthening the Epithelium and Modulating Gut Microbiota. Wang J. Frontiers in Microbiology

Uterine Microbiome

Commentary: Uterine Microbiota: Residents, Tourists, or Invaders?Altmäe S. Frontier in Immunology.

Technique

Preservation of microbial DNA in marine sediments: Insights from extracellular DNA pools. Torti A. Environmental Microbiology

REVIEW: Hypothesis Testing and Statistical Analysis of Microbiome. Xia Y. Genes and Diseases

A Zero-inflated Beta-binomial Model for Microbiome Data Analysis.Hu T. Stat

September 11, 2018

Today’s Digest has a ton of reviews on human gut microbiome, and also features a new bacterial growth theory, how antibiotics limit microbial metabolites penetrate the gut and discovery of bacteria from corals that inhibit the growth of a human pathogen.

General microbiology

Microbial exposure and human health – Anukriti Sharma & Jack A Gilbert – Current Opinion in Microbiology

** Consistent microbial dynamics and functional community patterns derived from first principles – Hadrien Delattre et al. – ISME J

Preprint: The Helicobacter pylori biofilm involves a multi-gene stress-biased response including a structural role for flagella – Skander Hathroubi et al. – bioRxiv

Human gut microbiome

Review: The intestinal epithelial response to damage – Laura Weichselbaum & Ophir D. Klein – Science China Life Sciences

Review: Metabolic Abnormalities in Diabetes and Kidney Disease: Role of Uremic Toxins – Laetitia Koppe et al. – Current Diabetes Reports

Sex differences in lipid metabolism are affected by presence of the gut microbiota – Annemarie Baars et al. – Scientific Reports

Age-dependent changes in GI physiology and microbiota: time to reconsider? – Ran An & Ellen Wilms et al. – Gut

Review: Bacteroides thetaiotaomicron – Nathan T. Porter et al. – Trends in Microbiology

** Antibodies Set Boundaries Limiting Microbial Metabolite Penetration and the Resultant Mammalian Host Response – Yasuhiro Uchimura et al. – Immunity

Review: Gut microbes as future therapeutics in treating inflammatory and infectious diseases: Lessons from recent findings – Suprabhat Mukherjee, Nikhilesh Joardar & Subhasree Sengupta et al. – The Journal of Nutritional Biochemistry

Review: A critical review on the impacts of β-glucans on gut microbiota and human health – Muthukumaran Jayachandran et al. – The Journal of Nutritional Biochemistry

Review: The microbiome in inflammatory bowel disease: from prevailing clinical evidence to future possibilities – Hari K. Somineni & Subra Kugathasan – Clinical Gastroenterology and Hepatology

Review: Influence of Early Life, Diet, and the Environment on the Microbiome – Tien S. Dong & Arpana Gupta – Clinical Gastroenterology and Hepatology

Review: Emerging Role of the Gut Microbiome in Nonalcoholic Fatty Liver Disease: From Composition to Function – S.R. Sharpton et al. – Clinical Gastroenterology and Hepatology

Preprint: Treatment-Specific Composition of Gut Microbiota Is Associated with Disease Remission in a Pediatric Crohn’s Disease Cohort – Daniel Sprockett et al. – bioRxiv

Human gut-microbiome-brain axis

Targeting the gut microbiota to influence brain development and function in early life – Shugui Wang et al. – Neuroscience & Biobehavioral Reviews

Human vaginal microbiome

Vaginal Bifidobacterium breve for preventing urogenital infections: development of delayed release mucoadhesive oral tablets – Barbara Giordani et al. – International Journal of Pharmaceutics

Animal experiments

Gut microbiota regulates mouse behaviors through glucocorticoid receptor pathway genes in the hippocampus – Yuanyuan Luo et al. – Translational Psychiatry

Review: Microbiome profiling reveals gut dysbiosis in a transgenic mouse model of Huntington’s disease – Geraldine Kong et al. – Neurobiology of Disease

Animal microbiome

Influence of the symbiont Wolbachia on life history traits of the cabbage root fly (Delia radicum) – Valérie Lopez et al. – Journal of Invertebrate Pathology

Letter to editor: Towards the integrative analysis of tick microbiome – Agustín Estrada-Peña & Alejandro Cabezas-Cruz – Ticks and Tick-borne Diseases

Plant, root and soil microbiome

Impact of domestication on the evolution of rhizomicrobiome of rice in response to the presence of Magnaporthe oryzae – Shaohua Shi et al. – Plant Physiology and Biochemistry

Microbiome Diversity in Cotton Rhizosphere Under Normal and Drought Conditions – Abid Ullah & Adnan Akbar et al. – Microbial Ecology

Characterization of microbial communities of soils from gold mine tailings and identification of mercury-resistant strain – Hongbing Ji et al. – Ecotoxicology and Environmental Safety

Plant-microbe competition: does injection of isotopes of C and N into the rhizosphere effectively characterise plant use of soil N? – Paul W. Hill & Davey L. Jones – New Phytologist

Water and extremophile microbiome

Temperature shapes the microbiota in anaerobic digestion and drives efficiency to a maximum at 45 °C – Sebastian Hupfauf et al. – Bioresource Technology

** Ruegeria sp. Strains Isolated from the Reef-Building Coral Galaxea fascicularis Inhibit Growth of the Temperature-Dependent Pathogen Vibrio coralliilyticus – Natsuko Miura et al. – Marine Biotechnology

Phages and viruses

Preprint: Potential application of phage therapy for prophylactic treatment against Pseudomonas aeruginosa biofilm Infections – Aditi Gurkar et al. – bioRxiv

Technology

Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota – Gregory L. Medlock et al. – Cell Systems

Application of Bacillus velezensis NJAU-Z9 Enhanced Plant Growth Associated with Efficient Rhizospheric Colonization Monitored by qPCR with Primers Designed from the Whole Genome Sequence – Yang Zhang et al. – Current Microbiology

September 10, 2018

In the today’s digest: an article on detection limits and bias with DNA extraction kits and primer choice, a novel R package to analyze timeseries in the 16S microbiome data in perturbation studies, a study on how fecal microbiota transplantation induces changes in gut microbial and metabolomic profiles of pediatric ulcerative colitis patients, plus an invitation for the first worldwide online open access course via Twitter about science and microbiology starting October 2.

Event

Third Annual Microbiome Symposium at Stanford, September 24 at the Stanford Faculty Club, Palo Alto, CA.

Human gut microbiome

*Gut microbial and metabolomic profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients – David J Nusbaum – FEMS Microbiology Ecology

Review: Sample preparation and recent trends in volatolomics for diagnosing gastrointestinal diseases – Tomasz Majchrzak – TrAC Trends in Analytical Chemistry

Special Report: The role of gut microbiota in lupus: what we know in 2018? – Lorena Ruiz – Expert Review of Clinical Immunology

Human gut virome

The Intestinal Virome and Immunity – Jessica A. Neil and Ken Cadwell – J Immunology

Human lung microbiome

The Human Respiratory Microbiome: The End of the Beginning? – Alicia B. Mitchell and Allan R. Glanville – Essentials in Lung Transplantation

Human oral microbiome

Review: The oral microbiome – friend or foe? – Kilian Mogens – Eur J Oral Science

Animal microbiome

Ultrahigh-throughput functional profiling of microbiota communities – Stanislav S. Terekhova – PNAS

Water microbiome

*Investigation of Detection Limits and the Influence of DNA Extraction and Primer Choice on the Observed Microbial Communities in Drinking Water Samples Using 16S rRNA Gene Amplicon Sequencing – Jakob Brandt and Mads Albertsen – Frontiers in Microbiology

Application of untargeted metabolomics for the detection of pathogenic Naegleria fowleri in an operational drinking water distribution system – Zhihao Yu – Water Research

Soil microbiome

Investigation on microbial community in remediation of lead-contaminated soil by Trifolium repensL. – Chenjing Liu – Ecotoxicology and Environmental Safety

Bioinformatics

*The Block Bootstrap Method for Longitudinal Microbiome Data – Pratheepa Jeganathan – arXiv

*Course

#EUROmicroMOOC: Trends in Microbiology [The first worldwide online open access microbiology course via Twitter]