Category Archives: Microbial Ecology

September 18, 2018

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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

 

 

September 15, 2018

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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

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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 8, 2018

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Have a nice weekend! Today, in Microbiome Digest: an interesting study remarking the importance of personalization in the efficient use of probiotics, given their individualized impact in gut microbiota (Zmora et al., Cell); another interesting paper about the application of autologous FMT in patients in Post-Antibiotic use and a worsening effect of Probiotics (Suez et al., Cell). Today, we have also papers about the dysbiosis in coronary artery disease, a metagenome of the female reproductive tract, a trial about the role of antibiotics in IBS risk and more!

Human and General Microbiome

Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT – Jotham Suez – Cell

Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features – Niv Zmora – Cell

The metagenome of the female upper reproductive tract – Chen Chen – GigaScience

Dysbiosis signatures of gut microbiota in coronary artery disease – Qi Zhu – Physiological Genomics

Review: The immunomodulatory role of probiotics in allergy therapy – Jafar Hajavi – Journal of Cellular Physiology

Efficient isolation and observation of the most complex human commensal, Demodex spp. – B. M. Clanner-Engelshofen – Experimental and Applied Acarology

Research Highlight: Boost microbiota studies – Wenjie Sun – Nature Nanotechnology

Reliability of a participant-friendly fecal collection method for microbiome analyses: a step towards large sample size investigation – Joanna W. Szopinska – BMC Microbiology

Alterations and structural resilience of the gut microbiota under dietary fat perturbations – Cong Liu – The Journal of Nutritional Biochemistry

Antibiotics: a risk factor for irritable bowel syndrome in a population-based cohort – Laura Rindom Krogsgaard – Scandinavian Journal of Gastroenterology

Inter-relationship between diet, lifestyle habits, gut microflora, and the equol-producer phenotype: baseline findings from a placebo-controlled intervention trial – Remi Yoshikata – Menopause

Review: Effects of Sourdough on FODMAPs in Bread and Potential Outcomes on Irritable Bowel Syndrome Patients and Healthy Subjects – Leidiane A. A. Menezes – Frontiers in Microbiology

Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization – Hsin-Wen Chang – Microbiome

 

Animal Microbiome / Animal Experiments

Early-life exposure to gut microbiota from disease protected mice does not impact disease outcome in type 1 diabetes susceptible NOD mice – Jane A. Mullaney – Immunology and Cell Biology

Shifts in the Skin-Associated Microbiota of Hatchery-Reared Common Snook Centropomus undecimalis During Acclimation to the Wild – Andrea M. Tarnecki – Microbial Ecology

Habitat environments impacted the gut microbiome of long-distance migratory swan geese but central species conserved – Yueni Wu – Scientific Reports

Effects of mixed lactic acid bacteria on intestinal microbiota of mice infected with Staphylococcus aureus – Dayong Ren – BMC Microbiology

Green tea polyphenols modify gut-microbiota dependent metabolisms of energy, bile constituents and micronutrients in female Sprague-Dawley rats – Jun Zhou – The Journal of Nutritional Biochemistry

Time-restricted feeding causes irreversible metabolic disorders and gut microbiota shift in pediatric mice – Dandan Hu – Pediatric Research

Compositional and predicted functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing – Zongfu Hu – PeerJ

The Effect of Co-infection of Food-Borne Pathogenic Bacteria on the Progression of Campylobacter jejuni Infection in Mice – Gang Wang – Frontiers in Microbiology

Structural and Functional Alterations in the Microbial Community and Immunological Consequences in a Mouse Model of Antibiotic-Induced Dysbiosis – Ying Shi – Frontiers in Microbiology

 

Plant Microbiome

Endophytic Bacterial Community Structure and Function of Herbaceous Plants From Petroleum Hydrocarbon Contaminated and Non-contaminated Sites – Rhea Lumactud – Frontiers in Microbiology

 

Environmental Microbiome

The effects of emerging environmental contaminants on Stenotrophomonas maltophilia isolated from drinking water in planktonic and sessile states – Inês B.Gomes – Science of The Total Environment

Genetic and Functional Diversity of Bacterial Microbiome in Soils With Long Term Impacts of Petroleum Hydrocarbons – Anna Gałązka – Frontiers in Microbiology

 

September 7, 2018

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Happy Friday everyone! Today’s digest covers microbiota dysbiosis in bowel obstruction, the soil microbial communities in apple orchards, and the bacterial and diatom composition of killer whale skin. Enjoy!

Human oral microbiome

Human defects in STAT3 promote oral mucosal fungal and bacterial dysbiosis – Abusleme – JCI Insight

High-resolution ISR amplicon sequencing reveals personalized oral microbiome – Mukherjee – Microbiome

Human gut microbiome

Review: Inflammasomes in the gastrointestinal tract: infection, cancer and gut microbiota homeostasis – Man – Nature Reviews Gastroenterology and Hepatology

Review: Norovirus interactions with the commensal microbiota – Sullender – PLoS Pathogens

Microbiota dysbiosis and its pathophysiological significance in bowel obstruction – Hegde – Scientific Reports

Microbiota-derived short-chain fatty acids promote Th1 cell IL-10 production to maintain intestinal homeostasis – Sun – Nature Communications

Animal experiments

Irreversible effects of trichloroethylene on the gut microbial community and gut-associated immune responses in autoimmune-prone mice – Khare – Journal of Applied Toxicology

Animal microbiome

Preprint: Efficacy of fecal sampling as a gut proxy in the study of chicken gut microbiota – Yan – BioRxiv

Preprint: Diet influences early microbiota development in dairy calves without long-term impacts on milk production – Dill-McFarland – BioRxiv

Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin – Hooper – Molecular Ecology

Plant, root, and soil microbiome

Diverse Bacteria Utilize Alginate Within the Microbiome of the Giant Kelp Macrocystis pyrifera – Lin – Frontiers in Microbiology

Spatial structuring of soil microbial communities in commercial apple orchards – Deakin – Applied Soil Ecology

Isolation and characterization of antagonistic bacteria with the potential for biocontrol of soil-borne wheat diseases – Wang – Journal of Applied Microbiology

Science, publishing, and career

Experimental technique isn’t my strong suit, but I can still be a scientist – Anderson – Science Careers

August 30, 2018

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Today’s digest covers population based studies on regional specificity of the gut microbiome, guidelines on use of fecal microbiota transplant, and review articles on role of the gut microbiome in colorectal cancer, liver tumors and functional gastrointestinal disorders. Also includes articles on how xenobiotics and psychotropic drugs affect the gut microbiota, and link to wonderful bacterial art!

General microbiome

Regional variation limits applications of healthy gut microbiome reference ranges and disease models – Yan He – Nature Medicine

Depicting the composition of gut microbiota in a population with varied ethnic origins but shared geography – Melanie Deschasaux – Nature Medicine

The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridium difficile infection and other potential indications: joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines – Benjamin H Mullish – Gut

Bile Acids, the Microbiome, Immunity, and Liver Tumors – Christoph Schramm – The New England Journal of Medicine

Review: The gut microbiome and colorectal cancer: a review of bacterial pathogenesis – Jessica D. Dahmus – Journal of Gastrointestinal Oncology

Human gut microbiome

Review: The Gut Microbiome in Adult and Pediatric Functional Gastrointestinal Disorders – Andrea Shin – Clinical Gastroenterology and Hepatology

Changes in microbiota composition, bile and fatty acid metabolism, in successful faecal microbiota transplantation for Clostridioides difficile infection – Jillian RM Brown – BMC Gastroenterology

“Cocktail” of Xenobiotics at Human Relevant Levels Reshapes the Gut Bacterial Metabolome in a Species-Specific Manner – Yingdan Zhang – Environmental Science and Technology

Animal experiments

Microbial Sensing by Intestinal Myeloid Cells Controls Carcinogenesis and Epithelial Differentiation – Naoteru Miyata – Cell Reports

Transplacental immune modulation with a bacterial-derived agent protects against allergic airway inflammation – Kyle T Mincham – Journal of Clinical Investigation

Differential effects of psychotropic drugs on microbiome composition and gastrointestinal function – Sofia Cussotto – Pschycopharmocology

Butyrate and Dietary Soluble Fiber Improve Neuroinflammation Associated With Aging in Mice – Stephanie M Matt – Frontiers in Immunonology

Correlations between intestinal innate immune genes and cecal microbiota highlight potential for probiotic development for immune modulation in poultry – Nicky-Lee Willson – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

Convergence between the microcosms of Southeast Asian and North American pitcher plants – Leonora S Bittleston – Elife

Water and extremophile microbiome 

In situ development of a methanotrophic microbiome in deep-sea sediments – S E Ruff – ISME Journal

Probiotics/Prebiotics

Probiotics for management of infantile colic: a systematic review of randomized controlled trials – Radoslaw Dryl – Archives of Medical Science

Bioinformatics

A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling – Ari Ugarte – Microbiome

Microbes in the news

The world’s smallest masterpieces? Microscopic version of Leonardo da Vinci’s Mona Lisa and portraits of Albert Einstein and Charles Darwin are recreated using MILLIONS of bacteria – Daily Mail

Non-microbiology picks 

Evaluating the replicability of social science experiments in Nature and Science between 2010 and 2015 – Colin F Camerer – Nature Human Behaviour

 

August 25 2018

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Todays Microbiome Digest covers the topics on microbiome of animalia kingdom ranging from humans ⇒mammals ⇒ amphibians ⇒ insects , cyanobacteria, AMR versus AMS, host microbe interactions, how & which microbes create homeostatis in the human body sites.  Happy Reading!

GUT or INTESTINAL MICROBIOME:

Gut microbiome: Microflora association with obesity and obesity-related comorbidities – Lone JB – Microb Pathog

Relevance of gut microbiota in cognition, behaviour and Alzheimer’s disease – de J R De-Paula V – Pharmacol Res.

Small intestinal microbiota: the neglected stepchild needed for fat digestion and absorption – Chang EB – Gut Microbes.

Prospects for Primary Prevention of Type 1 Diabetes by Restoring a Disappearing Microbe – Insel R – Pediatr Diabetes

ANIMAL MICROBIOME:

Synergetic action between the rumen microbiota and bovine health – Zeineldin M – Microb Pathog

Establishment of a Macaca fascicularis gut microbiome gene catalog and comparison with the human, pig and mouse gut microbiomes – Li X – Gigascience

Analyses of Aerosol Concentrations and Bacterial Community Structures for Closed Cage Broiler Houses at Different Broiler Growth Stages in Winter – Jiang L – J Food
Prot.

Characterization of the bacterial community of braised chicken, a specialty poultry product in China – Liu DY – Poult Sci.

Metagenomics analysis reveals significant modulation of cecal microbiota of broilers fed palm kernel expeller diets – Chen WL- Poult Sci.

Microbial diversity in the rumen, reticulum, omasum, and abomasum of yak on a rapid fattening regime in an agro-pastoral transition zone – Xue D – J Microbiol.

INSECT MICROBIOME:

Field-collected Triatoma sordida from central Brazil display high microbiota diversity that varies with regard to developmental stage and intestinal segmentation –
Oliveira JL – PLoS Negl Trop Dis.

FISH MICROBIOME:

Dietary salt levels affect digestibility, intestinal gene expression, and the microbiome, in Nile tilapia (Oreochromis niloticus) – Hallali E – PLoS One

WATER MICROBIAL ECOLOGY:

Bacterial bioclusters relate to hydrochemistry in New Zealand groundwater – Sirisena KA – FEMS Microbiol Ecol

 

PLANT MICROBIOME:

Technique : Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures – Cornet L – Microb Genom

High PAH degradation and activity of degrading bacteria during alfalfa growth where a contrasted active community developed in comparison to unplanted soil – Bourceret
A – Environ Sci Pollut Res Int.

 

INFANT MICROBIOME:

Investigating the effects of cesarean delivery and antibiotic use in early childhood on risk of later attention deficit hyperactivity disorder – Axelsson PB – J Child
Psychol Psychiatry

 

PROBIOTICS or PREBIOTICS:

The effect of a multispecies probiotic on microbiota composition in a clinical trial of patients with diarrhea-predominant irritable bowel syndrome – Hod K –
Neurogastroenterol Motil.

ANTI- MICROBIAL RESISTANCE and SUSCEPTANCE:

Un-segregated waste disposal: an alarming threat of antimicrobials in surface and ground water sources in Delhi – Velpandian T – Environ Sci Pollut Res Int.

Novel bioactive peptides from PD-L1/2, a type 1 ribosome inactivating protein from Phytolacca dioica L. Evaluation of their antimicrobial properties and anti-biofilm
activities – Pizzo E – Biochim Biophys Acta

 

RESPIRATORY MICROBIOME:

Lower airway microbiota for ‘biomarker’ measurements of cystic fibrosis disease progression – Sherrard LJ – Thorax

Sputum microbiota is predictive of long-term clinical outcomes in young adults with cystic fibrosis – Acosta N- Thorax

 

HOST MICROBE INTERACTIONS:

Preventive effects of bovine colostrum supplementation in TNBS-induced colitis in mice – Filipescu IE – PLoS One

Role of wnt5a in metabolic inflammation in humans – Relling I – J Clin Endocrinol Metab.

 

TECHNIQUES:

Review: Evidence-Based Strategies for the Prehabilitation of the Abdominal Wall Reconstruction Patient – Joslyn NA – Plast Reconstr Surg.

QMEC: a tool for high-throughput quantitative assessment of microbial functional potential in C, N, P, and S biogeochemical cycling – Zheng B – Sci China Life Sci.

Review: Advances in Imaging Specific Mediators of Inflammatory Bowel Disease – Dmochowska N – Int J Mol Sci.

 

NUTRITION or DIET and TREATMENT:

Glucomannan hydrolysate promotes gut proliferative homeostasis and extends lifespan in Drosophila melanogaster – Si Y – J Gerontol A Biol Sci Med Sci.

Cultivable butyrate-producing bacteria of elderly Japanese diagnosed with Alzheimer’s disease – Nguyen TTT – J Microbiol.

Efficacy of Proanthocyanidins from Pelargonium sidoides Root Extract in Reducing P. gingivalis Viability While Preserving Oral Commensal S. salivarius – Savickiene N –
Materials (Basel).

Effects of Tempeh Fermentation with Lactobacillus plantarum and Rhizopus oligosporus on Streptozotocin-Induced Type II Diabetes Mellitus in Rats – Huang YC – Nutrients

August 24, 2018

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Intra-individual microbiome biogeography, a review on IgA responses to the microbiota, seasonal fluctuations in the gut microbiota of white-faced capuchin monkeys, and the microbial composition of fog.

Pregnancy and early life

Sex-specific associations of infants’ gut microbiome with arsenic exposure in a US population – Anne G Hoen – Scientific Reports

Multi-site human microbiome

Assessing and Interpreting the Within-Body Biogeography of Human Microbiome Diversity – Zhanshan Ma – Frontiers in Microbiology

Human vaginal microbiome

Review: Investigating the effect of an abnormal cervico‐vaginal and endometrial microbiome on assisted reproductive technologies: A systematic review – Timothy Bracewell-Milnes – American Journal of Reproductive Immunology

Human gut microbiome

Review: IgA Responses to Microbiota – Jeffrey J Bunker – Immunity

Review: Comparing fecal microbiota transplantation to standard-of-care treatment for recurrent Clostridium difficile infection: a systematic review and meta-analysis – Muhammad Y Khan – European Journal of Gastroenterology & Hepatology

Animal experiments

Dietary L-Tryptophan Modulates the Structural and Functional Composition of the Intestinal Microbiome in Weaned Piglets – Haiwei Liang – Frontiers in Microbiology

Animal microbiome

Seasonality of the gut microbiota of free-ranging white-faced capuchins in a tropical dry forest – Joseph D Orkin – The ISME Journal

The microbiota in the intestinal and respiratory tracts of naked mole-rats revealed by high-throughput sequencing – Wei Cong – BMC Microbiology

Differential effects of selective and non-selective cyclooxygenase inhibitors on fecal microbiota in adult horses – Canaan M Whitfield-Cargile – PLOS ONE

Plant, root, and soil microbiome

Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems – Shuo Jiao – Microbiome

Fungal Communities Along a Small-Scale Elevational Gradient in an Alpine Tundra Are Determined by Soil Carbon Nitrogen Ratios – Yingying Ni – Frontiers in Microbiology

Water and extremophile microbiome

The biology of fog: results from coastal Maine and Namib Desert reveal common drivers of fog microbial composition – Sarah E Evans – Science of the Total Environment

Growth promotion and inhibition induced by interactions of groundwater bacteria – Patricia Geesink – FEMS Microbiology Ecology

Microbial diversity along a gradient in peatlands treating mining-affected waters – Katharina Kujala – FEMS Microbiology Ecology

Food microbiology

Volatile Flavor Components, Microbiota and Their Correlations in Different Sufu, a Chinese Fermented Soybean Food – Chunzhi Xiv – Journal of Applied Microbiology

Biogenic amines analysis and microbial contribution in traditional fermented food of Douchi – Lu Li – Scientific Reports

Changes in the microbial communities in vacuum-packaged smoked bacon during storage – Xinfu Li – Food Microbiology

Phages and viruses

MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins – Deyvid Amgarten – Frontiers in Genetics

Techniques

Comparative evaluation of a new magnetic bead-based DNA extraction method from fecal samples for downstream next-generation 16S rRNA gene sequencing – Kara D McGaughey – PLOS ONE

August 22, 2018

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Today’s digest is a mix of exciting reviews and research articles. The research articles are about – association between (site-specific) microbiota changes and stunded chilhood growth, bronchopulmonary dysplasia and Ankylosing Spondylitis; new tools to analyze mother-infant phage transmission; and low cost platform to analyze gut microbiota and host biomarkers. Also includes statement from FDA on regulation of live microbiome-based products, and comparison of single versus multiple strain probiotics in intestinal dysbiosis.

General microbiome

Review: Microbiology of the built environment – Jack A Gilbert – Nature Reviews Microbiology

Considerations for Best Practices in Studies of Fiber or Other Dietary Components and the Intestinal Microbiome – David M Klurfeld – American Journal of Physiology Endocrinology and Metabolism

Review: Impact of the commensal microbiota in atherosclerosis and arterial thrombosis – Klytaimnistra Kiouptsi – British Journal of Pharmacology

Pregnancy and early life

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome – Daniela SA Goltsman – bioRxiv

Human respiratory microbiome

Early Airway Microbial Metagenomic and Metabolomic Signatures are Associated with Development of Severe Bronchopulmonary Dysplasia – Charitharth V Lal – American Journal of Physiology

Human gut microbiome

Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa – Pascale Vonaesch – PNAS

Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX – Christian Milani – Microbiome

Altered Bacteria-Fungi Inter-Kingdom Network in Gut of Ankylosing Spondylitis Patients – Ming Li – bioRxiv

Animal experiments

Hyperactivated PI3Kd promotes self and commensal reactivity at the expense of optimal humoral immunity – Silvia Preite – Nature Immunology

The Potential Role of the Dipeptidyl Peptidase-4-Like Activity From the Gut Microbiota on the Host Health – Marta Olivares – Frontiers in Microbiology

Plant, root, and soil microbiome

Effects of compost containing oxytetracycline on enzyme activities and microbial communities in maize rhizosphere soil – Lisha Zhen – Environmental Science and Pollution Research

Impact of soil salinity on the microbial structure of halophyte rhizosphere microbiome – Salma Mukhtar – World Journal of Microbiology and Biotechnology

Water and extremophile microbiome

Inter-Kingdom beach warfare: Microbial chemical communication activates natural chemical defences – Zeinab G Khalil – The ISME Journal

Biogeography and taxonomic overview of terrestrial hot spring thermophilic phages – Olivier Zablocki – Extremophiles

Food microbiology

How Fine Structural Differences of Xylooligosaccharides and Arabinoxylooligosaccharides Regulate Differential Growth of Bacteroides Species – Mihiri Mendis – Journal of Agricultural and Food Chemistry

Probiotics / prebiotics

Influence of monostrain and multistrain probiotics on immunity, intestinal ultrastructure and microbiota in experimental dysbiosis – E Ermolenko – Beneficial Microbes

Effect of probiotic Bifidobacterium bifidum G9-1 on the relationship between gut microbiota profile and stress sensitivity in maternally separated rats – Hirokazu Fukui – Scientific Reports

Techniques

A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers – Melissa K Takahashi – Nature Communications

Microbes in the news

Statement from FDA Commissioner Scott Gottlieb, M.D., on advancing the science and regulation of live microbiome-based products used to prevent, treat, or cure diseases in humans – Food and Drug Administration

Non-microbiology picks

Mechanisms regulating intestinal barrier integrity and its pathological implications – Chaithanya Chelakkot – Experimental and Molecular Medicine

 

August 20, 2018

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Happy Monday! Today’s Microbiome Digest is chock-full. You’ll find: a review of approaches towards predictive microbial ecology, insights into function gleaned from rumen metatranscriptomics, diet studies in hunter-gatherers and mice, characterization of the mosquito and termite microbiota, the wild side of plant microbiomes, fermentation for traditional liquors, and much more!

General microbiome
Systems biology approaches towards predictive microbial ecology – Anne E. Otwell – Environmental Microbiology

One Health Relationships Between Human, Animal, and Environmental Microbiomes: A Mini-Review – Pauline Trinh – Frontiers in Public Health

Tuning of human MAIT cell activation by commensal bacteria species and MR1-dependent T-cell presentation – Cihan Tastan – Mucosal Immunology

Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation – Andrea Söllinger – mSystems

Multi-site human microbiome
A prospective study to examine the association of the urinary and fecal microbiota with prostate cancer diagnosis after transrectal biopsy of the prostate using 16sRNA gene analysis – Shaheen Alanee – Prostate

Streptococcus and Prevotella are associated with the prognosis of oesophageal squamous cell carcinoma – Yanfang Liu – Journal of Medical Microbiology

Urinary symptoms are associated with certain urinary microbes in urogynecologic surgical patients – Cynthia S. Fok – International Urogynecology Journal

Human gut microbiome
Links between environment, diet, and the hunter-gatherer microbiome – Gabriela K. Fragiadakis – Gut Microbes

Klebsiella oxytoca expands in cancer cachexia and acts as a gut pathobiont contributing to intestinal dysfunction – Sarah A. Pötgens – Scientific Reports

Co-Administration of Probiotics with Prescribed Antibiotics for Preventing Clostridium difficile Diarrhea – Ahmed S. I. Hamed – Academic Emergency Medicine

Animal experiments
Effect of industrial trans-fatty acids-enriched diet on gut microbiota of C57BL/6 mice – Yueting Ge – European Journal of Nutrition

AIEC infection triggers modification of gut microbiota composition in genetically predisposed mice, contributing to intestinal inflammation – Alexis Bretin – Scientific Reports

Effect of probiotic Bifidobacterium bifidum G9-1 on the relationship between gut microbiota profile and stress sensitivity in maternally separated rats – Hirokazu Fukui – Scientific Reports

Animal microbiome
Comparison of microbiomes of cold-water corals Primnoa pacifica and Primnoa resedaeformis, with possible link between microbiome composition and host genotype – Dawn B. Goldsmith – Scientific Reports

Neonatal gut and immune maturation is determined more by postnatal age than by post-conceptional age in moderately preterm pigs – Shuqiang Ren – American Journal of Physiology-Gastrointestinal and Liver Physiology

Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite –  Ning Liu – ISME Journal

Mosquito microbiota cluster by host sampling location – Ephantus J. Muturi – Parasites and Vectors

Plant, root, and soil microbiome|
The wild side of plant microbiomes – Juan E. Pérez-Jaramillo – Microbiome

Unraveling the Composition of the Root-Associated Bacterial Microbiota of Phragmites australis and Typha latifolia – Laura Pietrangelo – Frontiers in Microbiology

Vermicompost addition influences symbiotic fungi communities associated with leek cultivated in metal-rich soils – Antoine Pierart – Environmental Science and Pollution Research

Plant drought resistance is mediated by soil microbial community structure and soil-plant feedbacks in a savanna tree species – Nianxun Xi – Environmental and Experimental Botany

Metabolic specialization of denitrifiers in permeable sediments controls N2 O emissions – Hannah K. Marchant – Environmental Microbiology

Bacterial Biomarkers of Marcellus Shale Activity in Pennsylvania – Jeremy R. Chen See – Frontiers in Microbiology

Eighteen-Year Farming Management Moderately Shapes the Soil Microbial Community Structure but Promotes Habitat-Specific Taxa – Huaihai Chen – Frontiers in Microbiology

Water and extremophile microbiome
Bacterial and archaeal profiling of hypersaline microbial mats and endoevaporites, under natural conditions and methanogenic microcosm experiments – José Q. García-Maldonado – Extremophiles

Subsurface landfill leachate contamination affects microbial metabolic potential and their expression in the Banisveld aquifer – Neslihan Taş – FEMS Microbiology Ecology

Food microbiology
Robust Domination of Lactobacillus sakei in Microbiota During Traditional Japanese Sake Starter Yamahai-Moto Fermentation and the Accompanying Changes in Metabolites – Atsushi Tsuji – Current Microbiology

DaQu fermentation selects for heat resistant Enterobacteriaceae and bacilli – Zhiying Wang – Applied and Environmental Microbiology

Exploitation of autochthonous Tuscan sourdough yeasts as potential starters – Michela Palla – International Journal of Food Microbiology

Techniques
Conventional culture methods with commercially available media unveil the presence of novel culturable bacteria – Tamaki Ito – Gut Microbes