Category Archives: Human reproductive or urinary

July 04, 2018

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Today’s Digest is about association of the microbiome at various mucosal sites with different diseases in humans, germ-free chicken and microbial community in anoxic inter-tidal zone of Earth to study Lacustrine system of Mars. You can also read about BacStalk- software to analyze bacterial images, Chinese baby project and how air pollution is contributing to incidence of diabetes.

General microbiome

Review: Gut associated bacteria are critical to metabolism, inflammation and health – Philip Newsholme – Current Opinion in Clinical Nutrition and Metabolic Care

Review: The Microbiome and Acute Kidney Injury – H Rabb – Nephron

Multi-site human microbiome

Review: Cariogenic microbiome and microbiota of the early primary dentition: a contemporary overview – Kausar Sadia Fakhruddin – Oral Diseases

Dysbiosis of oral microbiota and its association with salivary immunological biomarkers in autoimmune liver disease – Kazumichi Abe – PlosOne

Human respiratory microbiome

Severe Obstructive Sleep Apnea is Associated with Alterations in the Nasal Microbiome and Increase in Inflammation – Benjamin G Wu – American Journal of Respiratory and Critical Care Medicine

Microbiota Composition and the Integration of Exogenous and Endogenous Signals in Reactive Nasal Inflammation – Francesco Antonio Salzano – Journal of Immunology Research

Human skin microbiome

Inflammatory cytokines and biofilm production sustain Staphylococcus aureus outgrowth and persistence: a pivotal interplay in the pathogenesis of Atopic Dermatitis – E.G.Di Domenico – Scientific reports

Human vaginal microbiome

Complex ecological interactions of Staphylococcus aureus in tampons during menstruation – Isaline Jacquemond – Scientific Reports

Human gut microbiome

Altered Intestinal Microbiota with Increased Abundance of Prevotella Is Associated with High Risk of Diarrhea-Predominant Irritable Bowel Syndrome – Tingting Su – Gastroenterology Research and Practice

The presence of genetic risk variants within PTPN2 and PTPN22 is associated with intestinal microbiota alterations in Swiss IBD cohort patients – Bahtiyar Yilmaz – PlosOne

Animal experiments 

Gut Microbial succession during conventionalization of germfree chicken – Thomas Milton – bioRxiv

Early-life antibiotics attenuate regulatory T cell generation and increase the severity of murine house dust mite-induced asthma – Alexander J. Adami – Pediatric Research

Changes in intestinal gene expression and microbiota composition during late pregnancy are mouse strain dependent – Marlies Elderman – Scientific Reports

Critical Roles for Microbiota-Mediated Regulation of the Immune System in a Prenatal Immune Activation Model of Autism – Catherine R. Lammert – The Journal of Immunology

Plant, root, and soil microbiome

Cascading effects of elevated ozone on wheat rhizosphere microbial communities depend on temperature and cultivar sensitivity – F. Changey – Environmental Pollution

Litter quality drives the differentiation of microbial communities in the litter horizon across an alpine treeline ecotone in the eastern Tibetan Plateau – Haifeng Zheng – Scientific Reports

Identification of a Novel Feruloyl Esterase by Functional Screening of a Soil Metagenomic Library – Xuanxuan Li – Applied Biochemistry and Biotechnology

Water and extremophile microbiome

Quorum sensing and iron regulate a two-for-one siderophore gene cluster in Vibrio harveyi – Darcy L. McRose – PNAS

Identifying labile DOM components in a coastal ocean through depleted bacterial transcripts and chemical signals – Alexey Vorobev – Environmental Microbiology

Metabolic potential of microbial communities from ferruginous sediments – Aurele Vuillemin – Environmental Microbiology

Microbes in space

The Microbial Community of a Terrestrial Anoxic Inter-Tidal Zone: A Model for Laboratory-Based Studies of Potentially Habitable Ancient Lacustrine Systems on Mars – Elliot Curtis-Harper – Microorganisms

Phages and viruses

Development of a high-throughput assay to detect antibody inhibition of low pH induced conformational changes of influenza virus hemagglutinin – Jessica F. Trost – PlosOne

Techniques

Review: Errors during Gene Expression: Single-Cell Heterogeneity, Stress Resistance, and Microbe-Host Interactions – Christpher R. Evans – mBio

BacStalk: a comprehensive and interactive image analysis software tool for bacterial cell biology – Raimo Hartmann – bioRxiv

Assessing the Mouse Intestinal Microbiota in Settings of Type-2 Immune Responses – Mei San Tang – Type 2 Immunity

Microbes in the news

Bacteria can ‘divide and conquer’ to vanquish their enemies – Science Daily

Gigantic study of Chinese babies yields slew of health data – Nature News

Non-microbiology picks

The 2016 global and national burden of diabetes mellitus attributable to PM2·5 air pollution – Benjamin Bowe – The Lancet Planetary Health

July 02, 2018

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Good morning! Today’s Microbiome Digest will cover the general microbiome, HIV infection and multi-site bacterial microbiota, crucial role of lung microbiome in asthma, gut microbiome in type 1 diabetes, Link between diet and metabolic syndrome, Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes, HmmUFOtu: a tool for taxonomic assignment and OTU picking and a news on plastic eating bacteria …

Events and jobs

Post-Doctoral Research Position, Oregon State University, with Dr. Stephen Giovannoni

Postdoctoral Researcher Position Characterizing Microbial Candidate Phlya at Stanford University

General microbiome

Issue: The microbiome: more than a gut reaction – John R. Wingard – Blood

Evaluation at scale of microbiome-derived metabolites as biomarker of flavan-3-ol intake in epidemiological studies – Javier I. Ottaviani – Scientific Reports

All disease begins in the gut: Influence of gastrointestinal disorders and surgery on oral drug performance – Grace B. Hatton – International Journal of Pharmaceutics

Designing microbial consortia with defined social interactions – Wentao Kong – Nature Chemical Biology

Multi-site human microbiome

HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa – Heidi Tuominen – Scientific Reports

Human respiratory microbiome

State of the Art: Does lung microbiome play a causal or casual role in asthma? – Maria Di Cicco – Pediatric Pulmonology

Human vaginal microbiome

Increased richness and diversity of the vaginal microbiota and spontaneous preterm birth – Aline C. Freitas – Microbiome

Human gut microbiome

Review: Gut microbiome in type 1 diabetes: A comprehensive review – Zheng P – Diabetes Metab Res Rev

Review: Altered Gut Microbiota: A Link Between Diet and the Metabolic Syndrome – Velasquez Manuel T – Metabolic Syndrome and Related Disorders

Chapter: Microbiota, Obesity and NAFLD – Louis H. S. Lau – Obesity, Fatty Liver and Liver Cancer

Chapter: The Influence of Gut Microbial Metabolism on the Development and Progression of Non-alcoholic Fatty Liver Disease – Wei Jia – Obesity, Fatty Liver and Liver Cancer

Method: Assessing the Mouse Intestinal Microbiota in Settings of Type-2 Immune Responses – Mei San Tang – Type 2 Immunity

Ancient Thali Diet: Gut Microbiota, Immunity, and Health – Kaitlyn Shondelmyer – Yale Journal of Biology & Medicine

Altered gut microbiome composition in children with refractory epilepsy after ketogenic diet – Yunjian Zhang – Epilepsy Research

The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut – Whitman B. Schofield – Cell Host & Microbe

Review: Update on the Gastrointestinal Microbiome in Systemic Sclerosis – Chiara Bellocchi – Current Rheumatology Reports

Review: The Gut Microbiome Alterations and Inflammation-Driven Pathogenesis of Alzheimer’s Disease—a Critical Review – Marta Sochocka – Molecular Neurobiology

The controversial role of Enterococcus faecalis in colorectal cancer – Carolina Vieira de Almeida – Therapeutic Advances in Gastroenterology

Animal experiments

Pea-protein alginate encapsulation adversely effects development of clinical signs of Citrobacter rodentium-induced colitis in mice treated with probiotics – Natallia Varankovich – Canadian Journal of Microbiology

Maternal Soluble Fiber Diet during Pregnancy Changes the Intestinal Microbiota, Improves Growth Performance, and Reduces Intestinal Permeability in Piglets – Chuanshang Cheng – Applied and Environmental Microbiology

Overlapping community composition of gut and fecal microbiomes in lab-reared and field-collected German cockroaches – Madhavi L. Kakumanu – Applied and Environmental Microbiology

TRIF deficiency protects non-obese diabetic mice from type 1 diabetes by modulating the gut microbiota and dendritic cells – Elke Gülden – Journal of Autoimmunity

Mucosal homeostasis is altered in the ileum of gnotobiotic mice – Chasen J. Greig – Journal of Surgical Research

Animal microbiome

Factors influencing bacterial microbiome composition in a wild non-human primate community in Taï National Park, Côte d’Ivoire – Jan F. Gogarten – The ISME Journal

Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes – Pablo Tsukayama – mSystems

Genetic variability and ontogeny predict microbiome structure in a disease-challenged montane amphibian – Sarah M. Griffiths – The ISME Journal

Plant, root, and soil microbiome

Review: Multifaceted Impacts of Bacteriophages in the Plant Microbiome – Britt Koskella – Annual Review of Phytopathology

‘Concord’ grapevine nutritional status and chlorosis rank associated with fungal and bacterial root zone microbiomes – R.W.Lewis – Plant Physiology and Biochemistry

Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil – Mobolaji F. Adegboye – Genome Announcements

Differences in microbial key players in anaerobic degradation between biogas and sewage treatment plants – Christian Buettner – International Biodeterioration & Biodegradation

Water and extremophile microbiome

The impact of the Deepwater Horizon blowout on historic shipwreck-associated sediment microbiomes in the northern Gulf of Mexico – Leila J. Hamdan – Scientific Reports

Stoichio-Metagenomics of ocean waters: a molecular evolution approach to trace the dynamics of nitrogen conservation in natural communities – Hannes Dittberner – Frontiers in Microbiology

 Probiotics / prebiotics

Review: Impact of Prebiotics on Poultry Production and Food Safety – Steven C. Ricke – Yale Journal of Biology & Medicine

Isolation and Partial Characterization of Lactic Acid Bacteria from the Gut Microbiota of Marine Fishes for Potential Application as Probiotics in Aquaculture – Sergio Alonso – Probiotics and Antimicrobial Proteins

Effects of Prebiotics vs a Diet Low in Fodmaps in Patients with Functional Gut Disorder – Jose-Walter Huaman – Gastroenterology

Bioinformatics

HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies – Qi Zheng – Genome Biology

Techniques

Review: Culturing the human microbiota and culturomics – Jean-Christophe Lagier – Nature Reviews Microbiology

Microbes in the news

Plastic-eating bacteria discovered by student could help solve global pollution crisis

Sewage microbes make a fuel booster

Our intestinal microbiome influences metabolism — through the immune system

 

Ashok’s non-microbiology picks

Efficacy and Safety of Dupilumab in Glucocorticoid-Dependent Severe Asthma – Klaus F. Rabe – The NEW ENGLAND JOURNAL of Medicine

June 30, 2018

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This Saturday enjoy reading and learning about effects of herbal chemicals on the modulation of cell metabolism, powerful Lactobacilli in vaginal environment or how halophylic bacteria can mitigate salt stress of halophytes. Happy weekend!

Human gut microbiome

Butyrate produced by gut commensal bacteria activates TGF-beta1 expression through the transcription factor SP1 in human intestinal epithelial cells – Camille Martin-Gallausiaux – Scientific reports

Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization – Matthew L. Jenior – mSphere

* Review: Novel therapeutic strategy for cancer and autoimmune conditions: Modulating cell metabolism and redox capacity – Xing-Xing Fan – Pharmacology & Therapeutics

Review: Gut microbiome and aging: Physiological and mechanistic insights – Ravinder Nagpal – Nutrition Healthy Aging

Editorial: Brain, antibiotics, and microbiota – how do they interplay? An Editorial for ‘Antibiotics‐induced modulation of large intestinal microbiota altered aromatic amino acid profile and expression of neurotransmitters in the hypothalamus of piglets’ – Elena Rybnikov – Journal of neurochemistry

Human vaginal microbiome

Randomized, placebo controlled phase I trial of safety, pharmacokinetics, pharmacodynamics and acceptability of tenofovir and tenofovir plus levonorgestrel vaginal rings in women – Andrea Ries Thurman – PLoS One

* Review: The Vaginal Microenvironment: The Physiologic Role of Lactobacilli – Emmanuel Amabebe – Frontiers in Medicine

Human lung microbiome

Profiling of lung microbiota in the patients with obstructive sleep apnea – Lu Dongmei – Medicine

Review: The consequence of matrix dysfunction on lung immunity and the microbiome in COPD – Tracy Hussell – European Respiratory Review

Water and extremophile microbiome

Tile Drainage and Anthropogenic Land Use Contribute to Harmful Algal Blooms and Microbiota Shifts in Inland Water Bodies – Igor Mrdjen – Environmental Science and Technology

Viral Communities of Shark Bay Modern Stromatolites – Richard Allen White III –
Frontiers in Microbiology

Plant, root, and soil microbiome

Changes in rhizosphere microbial communities in potted cucumber seedlings treated with syringic acid – Wang Z – PLoS One

* Bacterial microbiome of root-associated endophytes of Salicornia europaea in correspondence to different levels of salinity – Sonia Szymańska – Environmental Science and Pollution Research

Prebiotics

The Prebiotic Inulin Improves Substrate Metabolism and Promotes Short-Chain Fatty Acid Production in Overweight to Obese Men – Christina M. van der Beek – Metabolism

June 26, 2018

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Today’s Microbiome Digest cover the topics on bioinformatics; methods and models; trials and therapies; infection and immunity; microbiome of human gut, human vagina, insect, animals, plant, marine; food and nutrition; bioremediation and metabolomics.

 

EVENTS- JOBS – PhD POSITIONS:

Event – Organoids: Modelling Organ Development and Disease in 3D Culture – EMBO| EMBL Symposia

 

NEWS and VIEWS:

Pairing off: a bottom-up approach to the human gut microbiome– Clare Abreu – Molecular Systems Biology

 

BIOINFORMATICS:
Zero-inflated generalized Dirichlet multinomial regression model for microbiome compositional data analysis – Tang ZZ – Biostatistics

 

METHODS and MODELS:

Book Chapter – Methods for Microbiota Analysis: Sample Collection and Laboratory Methods – Saleh Ibrahim – The Microbiome in Rheumatic Diseases and Infection

Review: Culturing the human microbiota and culturomics – Lagier JC – Nature Reviews Microbiology

Using glycolysis enzyme sequences to inform Lactobacillus phylogeny – Katelyn Brandt – Microbial Genomics

Multicenter study establishing the clinical validity of a nucleic-acid amplification-based assay for the diagnosis of bacterial vaginosis – Cartwright CP – Diagnostics Microbiology and Infectious Disease.

PATENT – SYSTEM AND METHODS FOR DEVELOPING AND USING A MICROBIOME-BASED ACTION COMPONENT FOR PATIENT HEALTH – Warren Tracy, Jantzen Tammi Gregory Katherine

 

TRIALS and THERAPIES:

Antimicrobial photodynamic therapy as a new approach for the treatment of vulvovaginal candidiasis: preliminary results – Aline Silva Sousa – Lasers in Medical Science

Review – Prevention of Cystitis: Travelling between the Imaginary and Reality – Vecchio M – Annals of Nutrition and Metabolism

 

INFECTIONS and IMMUNITY:

Book Chapter – The Impact of Infections on Reproduction and Fertility – VE Jones – Clinical Reproductive Science

Intestinal barrier disruption and dysregulated mucosal immunity contribute to kidney fibrosis in chronic kidney disease – Yang J – Nephrology Dialysis Transplantation

In Press: Treatment and Prevention of Recurrent Lower Urinary Tract Infections in Women: A Rapid Review with Practice Recommendations – Ariana l Smith – The Journal of Urology

Book Chapter – Immunology of the Microbiome: Implications for Rheumatoid Arthritis and Other Autoimmune Diseases – Daniel M Altmann – The Microbiome in Rheumatic Diseases and Infection

 

VAGINAL MICROBIOME:

Description of three new Peptoniphilus species cultured in the vaginal fluid of a woman diagnosed with bacterial vaginosis: Peptoniphilus pacaensis sp. nov., Peptoniphilus raoultii sp. nov., and Peptoniphilus vaginalis sp. nov. – Diop K – Microbiology Open

 

GUT MICROBIOME: 

Preview – Gut microbiota as a missing link between nutrients and traits of human – Hea-Jong Chung – Frontiers in Microbiology

Preview – The gut-brain axis, the human gut microbiota and their integration in the development of obesity – Edward S Bliss – Frontiers in Microbiology

Review – The Gut Microbiome as a Target for the Treatment of Type 2 Diabetes – Ömrüm Aydin – Current Diabetes reports

Beneficial metabolic effects of 2’, 3’, 5’-tri-acetyl-N6-(3-hydroxylaniline) adenosine in multiple biological matrices and intestinal flora of hyperlipidemic hamsters– Tianqi Li – Journal of Proteome Research

 

ANIMAL MICROBIOME:

Preview – Dynamics of gut microbiota diversity during the early development of an avian host: evidence from a cross-foster experiment – Aimeric Teyssier – Frontiers in Microbiology

Enterococcus faecium WEFA23 from infant lessens high-fat-diet-induced hyperlipidemia via cholesterol 7-alpha-hydroxylase gene by altering the composition of gut microbiota in rats – Fuqing Huang – ScienceDirect

Evaluation of the impact of dental prophylaxis on the oral microbiota of dogs – Flancman R – PloS One

Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing – Ramesh J Pandit – Microbiome

 

GENERAL MICROBIOME:

Review – Role of nutrition, infection, and the microbiota in the efficacy of oral vaccines – Amrita Bhattacharjee – Clinical Science

Commensal Microbiota Enhance Both Osteoclast and Osteoblast Activities – Yoko Uchida – Molecules

 

PLANT/ROOT/SOIL MICROBIOME:

Editorial – The contribution of plant microbiota to economy growth – Angela Sessitsch – Microbial Biotechnology

Colonization cues of leaf- and root-inhabiting bacterial microbiota of Atractylodes lancea derived in vitro and in vivo – Yong Jia – Plant and Soil

Preview – Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism – Yuanchan Luo – – Frontiers in Microbiology

Genome Sequence of Bacillus megaterium Strain YC4-R4, a Plant Growth-Promoting Rhizobacterium Isolated from a HighSalinity Environment – Juan Ignacio Vílchez – GenomeAnnouncements

 

INSECT MICROBIOME:

Exposure of soil collembolans to microplastics perturbs their gut microbiota and alters their isotopic composition – DongZhu – Soil Biology and Biochemistry

 

SKIN MICROBIOME:

Book Chapter – Psoriasis and Psoriatic Arthritis – Madhura Castelino – The Microbiome in Rheumatic Diseases and Infection

 

MARINE MICROBIOME:
Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses – Felipe Hernandes Coutinho – Trends in Microbiology

 

NEONATAL/INFANT MICROBIOME:

Communication – Maternal Intrapartum Antibiotic Administration and Infantile Colic: Is there a Connection? – Leppälehto E – Neonatology

Review – Intrauterine Inflammation, Epigenetics, and Microbiome Influences on Preterm Infant Health – Lu L – Current Pathobiology Reports

 

CROSS – POPULATION MICROBIOME:
Similarities and differences in gut microbiome composition correlate with dietary patterns of Indian and Chinese adults – Abhishek Jain – AMB Express

 

PHAGES/VIRUSES:

Genome Sequence of the Pseudomonas protegens Phage GP100 – Jordan Vacheron – GenomeAnnouncements

 

FOOD and NUTRITION:

Plasma and urine metabolite profiling reveals the protective effect of Clinacanthus nutans in an ovalbumin-induced anaphylaxis model: 1H-NMR metabolomics approach – Leng Wei Khoo – Journal of Pharmaceutical and Biomedical Analysis

Drivers that establish and assembly the lactic acid bacteria biota in cheeses – Marco Gobbetti – Trends in Food Science & Technology

The food safety of DP-356Ø43 soybeans on SD rats reflected by physiological variables and fecal microbiota during a 90-day feeding study – Zou S – Regul Toxicol Pharmacol

Fermented Soybean Suppresses Visceral Fat Accumulation in Mice – Kushida M – Molecular Nutrition and Food Research

Combined Use of C. butyricum Sx-01 and L. salivarius C-1-3 Improves Intestinal Health and Reduces the Amount of Lipids in Serum via Modulation of Gut Microbiota in Mice – Long M – Nutrients

Review – Dietary polyphenols: A novel strategy to modulate microbiota-gut-brain axis – Diana Serra – Trends in Food Science & Technology

 

METABOLOMICS:

Non-invasive urinary metabolomic profiles discriminate biliary atresia from infantile hepatitis syndrome – Wei-Wei Li – Metabolomics

Metabolomics of the amniotic fluid: Is it a feasible approach to evaluate the safety of Chinese medicine during pregnancy? – Jinjun Shan – Journal of Applied Toxicology

Article – A validated, fast method for quantification of sterols and gut microbiome derived 5α/β-stanols in human faeces by isotope dilution LC-high resolution MS – Schoett HF – Analytical Chemistry

 

BIOREMEDIATION:

Bioprospecting for microbes with potential hydrocarbon remediation activity on the northwest coast of the Yucatan Peninsula, Mexico, using DNA sequencing – Mariela Beatriz Reyes-Sosa – Science of The Total Environment

 

ANTIBIOTIC SUSCEPTIBILITY:
Skin and nasal vestibule colonisation by Staphylococcus aureus and its susceptibility to drugs in atopic dermatitis patients – Wrobel J – Annals of Agriculture and Environmental Medicine

 

 

June 25, 2018

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Today’s Microbiome Digest features the sea turtle microbiome, the bacteria responsible for degrading bioplastics, a new clinical center for phage therapy, the gut-microbiome-brain axis in an Alzheimer’s Disease model, and a preprint about image duplication in scientific publishing.

Pregnancy and early life

Late-onset Sepsis in Preterm Infants Can Be Detected Preclinically by Fecal Volatile Organic Compound Analysis: A Prospective, Multicenter Cohort Study. – Daniel J C Berkhout- Clinical Infectious Diseases

Human vaginal microbiome

Abnormal vaginal microbioma is associated with severity of localized provoked vulvodynia. Role of aerobic vaginitis and Candida in the pathogenesis of vulvodynia. – Gilbert G. G. Donders- European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

* Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks – Filipe De Vadder – PNAS

Linking the Gut Microbiota to a Brain Neurotransmitter – Kelly G. Jameson – Trends in Neurosciences

Can epilepsy be treated by antibiotics? – Hilde M. H. Braakman – Journal of Neurology

* Changes in intestinal microbiota in HIV-1-infected subjects following cART initiation: influence of CD4+ T cell count – Yongjia Ji – Emerging Microbes & Infections

Review: Human gut microbiome: hopes, threats and promises – Patrice D Cani – Gut

Review: New treatments and therapeutic targets for IBS and other functional bowel disorders – Magnus Simrén – Nature Reviews Gastroenterology & Hepatology

Animal experiments

Effects of chronic noise exposure on the microbiome-gut-brain axis in senescence-accelerated prone mice: implications for Alzheimer’s disease – Bo Cui – Journal of Neuroinflammation

Bacterial methionine metabolism genes influence Drosophila melanogaster starvation resistance – Alec M. Judd – Applied and Environmental Microbiology

The benign helminth Hymenolepis diminuta ameliorates chemically induced colitis in a rat model system – Kateřina Jirků Pomajbíková – Parasitology

Protective role of commensal bacteria in Sjögren Syndrome – Mahira Zaheer – Journal of Autoimmunity

Lactobacillus murinus HF12 colonizes neonatal gut and protects rats from necrotizing enterocolitis. – Mubina Isani – PLOS One

Animal microbiome

Identification of bacteria present in ulcerative stomatitis lesions of captive sea turtles Chelonia mydas – D. X. Vega-Manriquez – Veterinary Research Communications

Characterization of the Microbiota of Oyster Larvae (Crassostrea virginica) and Tank Water from an Aquaculture System with High and Low Larval Survival Rates – Padmini Ramachandran – Genome Announcements

Early colonisation and temporal dynamics of the gut microbial ecosystem in Standardbred foals – S. Quercia – Equine Veterinary Journal

Plant, root, and soil microbiome

Microbial communities responsible for the degradation of poly(lactic acid)/poly(3-hydroxybutyrate) blend mulches in soil burial respirometric tests – Lenka Jeszeová – World Journal of Microbiology and Biotechnology

Phylogenetic diversity and investigation of plant growth-promoting traits of actinobacteria in coastal salt marsh plant rhizospheres from Jiangsu, China – Yuan Gong – Systematic and Applied Microbiology

Dynamics of soil microbial recovery from cropland to orchard along a 20-year chronosequence in a degraded karst ecosystem. – Hongkai Liao – Science of The Total Environment

Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling. – Margarita Lopez-Fernandez – FEMS Microbial Ecology

Distinct impacts of reductive soil disinfestation and chemical soil disinfestation on soil fungal communities and memberships. – Jun Zhao – Applied Microbiology and Biotechnology

* Dispersal-competition tradeoff in microbiomes in the quest for land colonization – Francisco Dini-Andreote – Scientific Reports

Water and extremophile microbiome

Linking patterns of net community production and marine microbial community structure in the western North Atlantic. – Seaver Wang – The ISME Journal

Probiotics/Prebiotics

Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans. – Kaarel Adamberg – Anaerobe

Review: Nutraceuticals in Colorectal Cancer: A Mechanistic Approach – Marco Rossi – European Journal of Pharmacology

Science, publishing, and career

* Analysis and Correction of Inappropriate Image Duplication: The Molecular and Cellular Biology Experience – Arturo Casadevall – bioRxiv

Microbes in the news

U.S. center will fight infections with viruses – Kelly Servick – Science

Alyson’s non-microbiology pick

Neanderthal brain organoids come to life – Jon Cohen – Science

June 22, 2018

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Have a happy weekend! Today in Microbiome Digest: reviews on microbiome immunity and type 1 diabetes,  metatranscriptome analysis of vaginal microbiome, Differences in gut microbiota associated with age, sex, and stool consistency, microbes in the news, and more…

Events and jobs

Scientist – Genomics and Microbiome – Madison, WI

Bioinformatics Scientific Programmer – Quadram Institute Bioscience

General microbiome

Review: Communication Between the Microbiota and Mammalian Immunity – Kyla S. Ost – Annual Review of Microbiology

Host genotype-specific microbiota do not influence the susceptibility of D. magna to a bacterial pathogen – Marilou P. Sison-Mangus – Scientific Reports

Pregnancy and early life

Book chapter: Implantation Failure 1: Intrauterine Circumstances and Embryo–Endometrium Synchrony at Implantation – Keiji Kuroda – Treatment Strategy for Unexplained Infertility and Recurrent Miscarriage

Special Issue: Microbiome in normal and pathological pregnancies: A literature overview – Carla R. Taddei – American Journal of Reproductive Immunology

Multi-site human microbiome

Bacterial invasion of dentinal tubules from the external root surface with and without an intact cemental layer- a confocal laser scanning microscopic study – Jovita D’souza – Advances in Tissue Engineering and Regenerative Medicine

Human respiratory microbiome

Review: Drug Resistance and Gene Transfer Mechanisms in Respiratory/Oral Bacteria – Jiang S – Journal of Dental Research

Ecology and diversity in upper respiratory tract microbial population structures from a cross-sectional community swabbing study –  Abigail L. Coughtrie – Journal of Medical Microbiology

Human skin microbiome

Skin Microbiota in Obese Women at Risk for Surgical Site Infection After Cesarean Delivery – Kara M. Rood – Scientific Reports

Human vaginal microbiome

Review: Pharmacology of Antiretrovirals in the Female Genital Track for HIV Prevention – Melanie R. Nicol – The Journal of Clinical Pharmacology

Metatranscriptome Analysis of the Vaginal Microbiota Reveals Potential Mechanisms for Protection against Metronidazole in Bacterial Vaginosis – Zhi-Luo Deng – mSphere 

Human gut microbiome

Review: Gut microbiome in type 1 diabetes: A comprehensive review – Zheng P – Diabetes/Metabolism Research and Reviews

A Small Molecule-Screening Pipeline to Evaluate the Therapeutic Potential of 2-Aminoimidazole Molecules Against Clostridium difficile – Thanissery R – Frontiers in Microbiology

Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects – Tomohisa Takagi – Journal of Gastroenterology

Dietary Supplementation with a Magnesium-Rich Marine Mineral Blend Enhances the Diversity of Gastrointestinal Microbiota – Erin K. Crowley – Marine Drugs

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms – Brandon Brooks – Microbiome

Review: Potential Role of the Gut Microbiome in ALS: A Systematic Review – Michelle L. Wright – Biological Research for Nursing

Animal experiments

Lack of liver steatosis in germ-free mice following hypercaloric diets – Stephan C. Bischoff – European Journal of Nutrition

 Plant, root, and soil microbiome

Exploring Elicitors of the Beneficial Rhizobacterium Bacillus amyloliquefaciens SQR9 to Induce Plant Systemic Resistance and Their Interactions With Plant Signaling Pathways – Gengwei Wu – Molecular Plant-Microbe Interactions

Correlation and Distribution of Xenobiotics Genes and Metabolic Activities with Level of Total Petroleum Hydrocarbon in Soil, Sediment and Estuary Water in the Niger Delta Region of Nigeria – U. O. Edet – Asian Journal of Biotechnology and Genetic Engineering

Review: Status and future of disease protection and grape berry quality alteration by microorganisms in viticulture – Misa Otoguro – Letters in Applied Microbiology

Editorial: The contribution of plant microbiota to economy growth – Angela Sessitsch – Microbial Biotechnology

Water and extremophile microbiome

Mini-Review: Future direction in marine bacterial agarases for industrial applications -Saeid Tamadoni Jahromi – Applied Microbiology and Biotechnology

Prokaryotic assemblages in the maritime Antarctic Lake Limnopolar (Byers Peninsula, South Shetland Islands) – M. Papale – Extremophiles

Taxonomy, phylogeny and ecology of cultivable fungi present in seawater gradients across the Northern Antarctica Peninsula – Vívian N. Gonçalves – Extremophiles 

A strong link between marine microbial community composition and function challenges the idea of functional redundancy – Pierre E. Galand – The ISME Journal

Probiotics / prebiotics

Gut Microbiota, Probiotics, and Sport: From Clinical Evidence to Agonistic Performance – Marco Pane – Journal of Clinical Gastroenterology

 Microbes in the news

‘Green’-feed: Industrial microbes could feed cattle, pigs, chicken

SMU researchers hope microbes will lead them to strike oil offshore

Scientists Reveal How Gut Microbes ‘Recover’ After Antibiotic Treatment

Celebrate your gut microbiota on the first World Microbiome day!

 Microbes on the market (news about biotech companies)

Human Microbiome Market – Global Industry Analysis, Size, Share, Growth, Trends, and Forecast 2018 – 2026

MaaT Pharma and Lutech Sign Licensing Agreement on Microbiome Therapy for Graft-vs-Host Disease

 

Ashok’s non-microbiology picks

The Rheumatoid Arthritis-Associated Citrullinome – Ronak Tilvawala – Cell Chemical Biology

Inflammation-Induced, STING-Dependent Autophagy Restricts Zika Virus Infection in the Drosophila Brain – Yuan Liu – Cell Host & Microbe

Distinct progenitor lineages contribute to the heterogeneity of plasmacytoid dendritic cells – Patrick Fernandes Rodrigues – Nature Immunology

A synaptic threshold mechanism for computing escape decisions – Dominic A. Evans – Nature

June 18, 2018

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Have a good Monday! Today in Microbiome Digest: reviews about the relationship between microbiome and brain function, vaccine response and dermatology. Studies about psoriasis and the gut microbiology, the effect of osmotic changes on the gut microbiota, protocols for oral microbiota profiling in lab classes, the role of indole in gut inflammation and more…

Human and General Microbiome

Review: Bile acids and FXR in functional gastrointestinal disorders – Paula Mosińska – Digestive and Liver Disease

Review: The Microbiome in Psychology and Cognitive Neuroscience – Amar Sarkar – Trends in Cognitive Sciences

Review: The influence of the intestinal microbiome on vaccine responses – Petra Zimmermann – Vaccine

Review: Close Encounters of Three Kinds: Bacteriophages, Commensal Bacteria, and Host Immunity – Eric C. Keen – Trends in Microbiology

The microbiome in dermatology – Shenara Musthaq – Clinics in Dermatology

Is psoriasis a bowel disease? Successful treatment with bile acids and bioflavonoids suggests it is – P. Haines Ely – Clinics in Dermatology

Microbial markers in colorectal cancer detection and/or prognosis – Romain Villéger – World Journal of Gastroenterology

Neurotransmitter modulation by the gut microbiota – Philip Strandwitz – Brain Research

Intestinal microbiota assessment in cirrhotic patients from a Mexican mestizo population – C. Pérez-Monter – Revista de Gastroenterología de México (Article in Spanish)

Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China – Peng Wu – Frontiers in Cellular and Infection Microbiology

Analysis of human C24 bile acids metabolome in serum and urine based on enzyme digestion of conjugated bile acids and LC-MS determination of unconjugated bile acids – Pingping Zhu – Analytical and Bioanalytical Chemistry

Tobacco-smoking-related prevalence of methanogens in the oral fluid microbiota – Ghiles Grine – Scientific Reports

Effect of rectal douching/enema on rectal gonorrhoea and chlamydia among a cohort of men who have sex with men on HIV pre-exposure prophylaxis – Adiba Hassan – Sexually Transmitted Infections

Effect of administration of a probiotic preparation on gut microbiota and immune response in healthy women in India: an open-label, single-arm pilot study – Ankita Singh – BMC Gastroenterology

The urinary microbiome in women with mixed urinary incontinence compared to similarly aged controls – Yuko M. Komesu – International Urogynecology Journal

The influence of in vitro pectin fermentation on the human fecal microbiome – So-Jung Bang – AMB Express

Host genetics and microbiome associations through the lens of genome wide association studies – Omer Weissbrod – Current Opinion in Microbiology

Cutibacterium acnes and the shoulder microbiome – Boyang Qiu – Journal of Shoulder and Elbow Surgery

 

Animal Microbiome / Animal Experiments

Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota – Carolina Tropini – Cell

Probiotics L. acidophilus and B. clausii Modulate Gut Microbiota in Th1- and Th2-Biased Mice to Ameliorate Salmonella Typhimurium-Induced Diarrhea – Biswaranjan Pradhan – Probiotics and Antimicrobial Proteins

Altered microRNA regulation of short chain fatty acid receptors in the hypertensive kidney is normalized with hydrogen sulfide supplementation – Gregory J. Weber – Pharmacological Research

The effect of antibiotics on social aversion following early life inflammation – Amanda C. Kentner – Physiology & Behavior

Analysis of the Gut Microbial Diversity of Dairy Cows During Peak Lactation by PacBio Single-Molecule Real-Time (SMRT) Sequencing – Weicheng Li – Current Microbiology

Diet Modifies Colonic Microbiota and CD4+ T Cell Repertoire to Induce Flares of Colitis in Mice With Myeloid-cell Expression of Interleukin 23 – Lili Chen – Gastroenterology

Chronic exposure to fungicide propamocarb induces bile acid metabolic disorder and increases trimethylamine in C57BL/6J mice – Sisheng Wu – Science of The Total Environment

Distribution of Salmonella Enteritidis in internal organs and variation of cecum microbiota in chicken after oral challenge – Jinxin Zeng – Microbial Pathogenesis

The comparative genomics of Bifidobacterium callitrichos reflects dietary carbohydrate utilization within the common marmoset gut – Korin Albert – Microbial Genomics

The gut microbiota metabolite indole alleviates liver inflammation in mice – Martin Beaumont – The FASEB Journal

Alpha-Ketoglutarate in Low-Protein Diets for Growing Pigs: Effects on Cecal Microbial Communities and Parameters of Microbial Metabolism – Jiashun Chen – Frontiers in Microbiology

Berberine Regulates Treg/Th17 Balance to Treat Ulcerative Colitis Through Modulating the Gut Microbiota in the Colon

Screening of multimeric β-xylosidases from the gut microbiome of a higher termite, Globitermes brachycerastes – Huantian Cui – Frontiers in Pharmacology

Impact of Gut Microbiota and Diet on the Development of Atherosclerosis in Apoe-/- Mice – Annika Lindskog Jonsson – Arteriosclerosis, Thrombosis, and Vascular Biology

Saturated long-chain fatty acid-producing bacteria contribute to enhanced colonic motility in rats – Ling Zhao – Microbiome

News in Brief: Antibiotics Protect Against Liver Tumors in Mice in Cancer Discovery

 

Water Microbiome

Methanogenic community shifts during the transition from sewage mono-digestion to co-digestion of grass biomass – Justus Hardegen – Bioresource Technology

 

Protocols and Methodologies

Simple Protocol for Molecular Fingerprinting of Human Oral Microbiota Samples in Lab Classes – Ana C. Henriques – Journal of Microbiology & Biology Education

Sample tracking in microbiome community profiling assays using synthetic 16S rRNA gene spike-in controls – Dieter M. Tourlousse – Scientific Reports

Taxonomy-aware feature engineering for microbiome classification – Mai Oudah – BMC Bioinformatics

 

June 13, 2018

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Events and jobs

Computational scientists (from post-master to postdoc fellowships) in metagenomics and microbial genomics : Trento, Italy – The Laboratory of Computational Metagenomics

General microbiome

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative – Jun Wang, Microbiome Announcement

Microbial ecology

Everything is not everywhere: a tale on the biogeography of cyanobacteria – Karine Felix Ribeiro, Hydrobiologia

A Meta‐Analysis of Temperature Sensitivity as a Microbial Trait – Charlotte J. Alster, Global Change Biology

Microbial island biogeography: isolation shapes the life history characteristics but not diversity of root-symbiotic fungal communities – John Davison, ISME

Bacillus thuringiensis produces the lipopeptide thumolycin to antagonize microbes and nematodes – Dehong Zheng, Microbiological Research

Qualitative analysis of biosurfactants from Bacillus species exhibiting antifungal activity – Ambrin Sarwar, Plos One

Antarctic cryptoendolithic fungal communities are highly adapted and dominated by Lecanoromycetes and Dothideomycetes – Claudia Coleine, Frontiers in Microbiology

Pregnancy and early life

The Microbiome and Metabolome of Preterm Infant Stool Are Personalized and Not Driven by Health Outcomes, Including Necrotizing Enterocolitis and Late-Onset Sepsis – Stephen Wandro, mSphere

The role of breast milk in the colonization of neonatal gut and skin with coagulase-negative staphylococci – Hiie Soeorg, Pediatric Research

Multisite human microbiome

Prion-like Propagation of α-synuclein in the gut-brain axis – Ying Chen, Brain Research Bulletin

Microbiome-Gut-Brain Axis and Toll-Like Receptors in Parkinson’s Disease – Valentina Caputi, International Journal of Molecular Sciences

Current Insights in Microbiome Shifts in Sjogren’s Syndrome and Possible Therapeutic Interventions – Christina Tsigalou, Frontiers in Immunology

Comparison of Infant Gut and Skin Microbiota, Resistome and Virulome between Neonatal Intensive Care Unit (NICU) Environments – Suchitra K. Hourigan, Frontiers in Microbiology

Human skin microbiome

Skin Microbiota in Obese Women at Risk for Surgical Site Infection After Cesarean Delivery – Kara M. Rood, Scientific Reports

Cutibacterium acnes (Propionibacterium acnes) and acne vulgaris: a brief look at the latest updates – B. Dréno, Journal of the European Academy of Dermatology and Venereology

Characterisation of Cutibacterium acnes phylotypes in acne and in vivo exploratory evaluation of Myrtacine® – S. Pécastaings, Journal of the European Academy of Dermatology and Venereology

Human oral microbiome

Analysis of the oral microbiome on the surface of modified dental polymers – Denise  Tornavoi de Castro, Archives of Oral Biology

Genetic Association with Subgingival Bacterial Colonization in Chronic Periodontitis – Franco Cavalla, Genes

Biological and cultural drivers of oral microbiota in Medieval and Post-Medieval London, UK – Andrew G Farrer, bioRxiv

Human gut microbiome

Breath methane concentrations and markers of obesity in patients with functional gastrointestinal disorders – Clive H. Wilder-Smith, United European Gastroenterology Journal

The Intersection Between Colonization Resistance, Antimicrobial Stewardship, and Clostridium difficile – Rossana Rosa, Current Infectious Disease Reports

Celiac Disease and Fecal Microbiota Transplantation: A New Beginning? – Shmuel Golfeyz MD, Correspondence

Gut microbiota metabolites, amino acid metabolites and improvements in insulin sensitivity and glucose metabolism: the POUNDS Lost trial – Yoriko Heianza, Nutrition

Cutting the Gordian Knot of the Microbiota – Kimberly S.Vasquez, Molecular Cell

Host: Microbiome co-metabolic processing of dietary polyphenols – An acute, single blinded, cross-over study with different doses of apple polyphenols in healthy subjects – Kajetan Trost, Food Research International

Clinical trials of kimchi intakes on the regulation of metabolic parameters and colon health in healthy Korean young adults – Hee-Young Kim, Journal of Functional Foods

Animal experiments

Propolis from Different Geographic Origins Suppress Intestinal Inflammation in a Model of DSS‐Induced Colitis is Associated with Decreased Bacteroides spp. in the Gut – Kai Wang, Molecular Nutrition and Food Research

Effect of direct-fed microbials on culturable gut microbiotas in broiler chickens: a meta-analysis of controlled trials – Chhaiden Heak, Asian-Australasian Journal of Animal Sciences

A dietary isothiocyanate-enriched moringa (Moringa oleifera) seed extract improves glucose tolerance in a high-fat-diet mouse model and modulates the gut microbiome – Asha Jaja-Chimedza, Journal of Functional Foods

The enteric microbiota regulates jejunal Paneth cell number and function without impacting intestinal stem cells – Alexi A. Schoenborn, Gut Microbes

Comprehensive longitudinal microbiome analysis of the chicken cecum reveals a shift from competitive to environmental drivers and a window of opportunity for Campylobacter – Umer Zeeshan Ijaz, bioRxiv

Microbial quantity impacts Drosophila nutrition, development, and lifespan – Erin S. Keebaugh, iScience

Absence of Gut Microbiota Reduces Emotional Reactivity in Japanese Quails (Coturnix japonica) – Narjis Kraimi, Frontiers in Physiology

Animal microbiome

Identification of circular single-stranded DNA viruses in faecal samples of Canada lynx (Lynx canadensis), moose (Alces alces) and snowshoe hare (Lepus americanus) inhabiting the Colorado San Juan Mountains – Simona Kraberger, Infection, Genetics and Evolution

Diverse novel resident Wolbachia strains in Culicine mosquitoes from Madagascar – Claire L Jeffries, bioRxiv

Sample treatment optimization for fish stool metabolomics – Takeshi Hano, Journal of Chromatography B

Plant, root, and soil microbiome

Two decades of altered snow cover does not affect soil microbial ability to catabolize carbon compounds in an oceanic alpine heath – E.R. Jasper Wubs, Soil Biology and Biochemistry

Grazing and resource availability control soil nematode body size and abundance‐mass relationship in semi‐arid grassland – W. S. Andriuzzi, Journal of Animal Ecology

Isolation and screening of antibiotic producing actinomycetes from rhizosphere and agricultural soils – Atsede Muleta, African Journal of Biotechnology

Responses of Bougainvillea spectabilis to elevated atmospheric CO2 under galaxolide (HHCB) pollution and the mechanisms of its rhizosphere metabolism – Minzhe Zhang, Journal of Soils and Sediments

Differential effect of the nitrogen form on the leaf gas exchange, amino acid composition, and antioxidant response of sweet pepper at elevated CO2 – María C. Piñero, Plant Growth Regulation

Viral metagenomics analysis and eight novel viral genomes identified from the Dushanzi mud volcanic soil in Xinjiang, China – Dan-Ting Yu, Journal of Soils and Sediments

Efficacy of Bacillus subtilis native strains for biocontrol of Phytophthora crown and root rot of pistachio in Iran – Mohammad Moradi, Tropical Plant Pathology

Modification of plant cell wall chemistry impacts metabolome and microbiome composition in Populus PdKOR1 RNAi plants – Allison M. Veach, Plant and Soil

Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities – Sai Guo, European Journal of Soil Biology

Microbial communities and natural fermentation of corn silages prepared with farm bunker-silo in Southwest China – Hao Guan, Bioresource Technology

Cultivated methanotrophs associated with rhizospheres of traditional rice landraces from Western India belong to Methylocaldum and Methylocystis – Monali C. Rahalkar, 3 Biotech

Metal(loid)-resistant bacteria reduce wheat Cd and As uptake in metal(loid)-contaminated soil – Xiao-Han Wang, Environmental Pollution

Enhanced removal of nitrate in the maize rhizosphere by plant growth-promoting Bacillus megaterium NCT-2, and its colonization pattern in response to nitrate – Shaohua Chu, Chemosphere

Bioactive luteoloside produced by Myroides odoratimimus, solvent-tolerant bacterium form the rhizosphere of Lonicera japonica –  Y. X. Zhao, Natural Product Research

Potential application of selected metal resistant phosphate solubilizing bacteria isolated from the gut of earthworm (Metaphire posthuma) in plant growth promotion – Jayanta  Kumar Biswas, Geoderma

Effects of Pseudomonas chenduensis and biochar on cadmium availability and microbial community in the paddy soil – Lingjuan Li, Science of The Total Environment

Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities – Sai Guo, European Journal of Soil Biology

Analysis on metabolic functions of stored rice microbial communities by BIOLOG ECO microplates – Zhiwen Ge, Frontiers in Microbiology

Effects of discrete bioactive microbial volatiles on plants and fungi – Birgit Piechulla, Plant, Cell, and Environment

Phylogenetic-scale disparities in the soil microbial diversity–ecosystem functioning relationship – Marta Goberna, ISME

Similar soil microbial community structure across different environments after long‐term succession: evidence from volcanoes of different ages – Shangqi Xu, Journal of Basic Microbiology

Water and extremophile microbiome

Comparison among the microbial communities in the lake, lake wetland, and estuary sediments of a plain river network – Wei Huang, Microbiology Open

The distinctive microbial community improves composting efficiency in a full-scale hyperthermophilic composting plant – Zhen Yu, Bioresource Technology

Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom – Ivan S. Mikhailov, Microbial Ecology

The Legacy Effects of Winter Climate on Microbial Functioning After Snowmelt in a Subarctic Tundra – Maria Väisänen, Microbial Ecology

Characterization of phototrophic microorganisms and description of new cyanobacteria isolated from the saline-alkaline crater-lake Dziani Dzaha (Mayotte, Indian Ocean) – M. Cellamare, FEMS Microbiology Ecology

Methanogens in the Antarctic Dry Valley Permafrost – Tatiana A. Vishnivetskaya, FEMS Microbiology Ecology

Bacterial Diversity in an Alpine Debris-Free and Debris-Cover Accumulation Zone Glacier Ice, North Sikkim, India – Mingma Thundu Sherpa, Indian Journal of Microbiology

Culturing the ubiquitous freshwater actinobacterial acI lineage by supplying a biochemical ‘helper’ catalase – Suhyun Kim, bioRxiv

Assessing the effect of pretreatments on the structure and functionality of microbial communities for the bioconversion of microalgae to biogas – Olivia Córdova, Frontiers in Microbiology

Great Salt Lake microbiology: a historical perspective – Bonnie K. Baxter, International Microbiology

Life from the ashes: survival of dry bacterial spores after very high temperature exposure – Lynda Beladjal, Extremophiles

Microbial and geochemical controls on waste rock weathering and drainage quality – Sharon Blackmore, Science of The Total Environment

Characterization and high-throughput sequencing of a trichlorophenol-dechlorinating microbial community acclimated from sewage sludge – Jiaxiu Song, Journal of Cleaner Production

Impacts of surface-applied residues on N-cycling soil microbial communities in miscanthus and switchgrass cropping systems – Karen A. Thompson, Applied Soil Ecology

Water is a critical factor in evaluating and assessing microbial colonization and destruction of Angkor sandstone monuments – Xiaobo Liu, International Biodeterioration & Biodegradation

Methanogenic community shifts during the transition from sewage mono-digestion to co-digestion of grass biomass – Justus Hardegen, Bioresource Technology

Bacterial lineages putatively associated with the dissemination of antibiotic resistance genes in a full-scale urban wastewater treatment plant – Carlos Narciso-da-Rocha, Environment International

Impact of organic waste composition on life cycle energy production, global warming and Water use for treatment by anaerobic digestion followed by composting – Sara A. Pace, Resources, Conservation and Recycling

1H NMR metabolomics of microbial metabolites in the four MW agricultural biogas plant reactors: A case study of inhibition mirroring the acute rumen acidosis symptoms – Boštjan Murovec, Journal of Environmental Management

Comparative Metagenomics Provides Insight into the Ecosystem Functioning of the Shark Bay Stromatolites, Western Australia – Joany Babilonia, Frontiers in Microbiology

Assessing the abundance of fungal populations in a full-scale membrane bioreactor (MBR) treating urban wastewater by using quantitative PCR (qPCR) – P. Maza-Márquez, Journal of Environmental Management

Food microbiology

Occurrence of lactic acid bacteria and yeasts at species and strain level during spontaneous fermentation of mawè, a cereal dough produced in West Africa – Marcel Houngbédji, Food Microbiology

Probiotics / prebiotics

Probiotics in IBD: Combining in vitro and in vivomodels for selecting strains with both anti-inflammatory potential as well as a capacity to restore the gut epithelial barrier – Mazen Zaylaa, Journal of Functional Foods

Can prebiotics assist in the management of cognition and weight gain in schizophrenia? – Amy Chia-Ching Kao, Psychoneuroendocrinology

Probiotic potentials of Lactobacillus plantarum isolated from fermented durian (Tempoyak), a Malaysian traditional condiment – Asmariah Ahmad, Food Science and Nutrition

Bioinformatics

Identifying Heritable Communities of Microbiome by Root-Unifrac and Wishart Distribution – Yunfan Tang, bioRxiv

PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive – Pedro J. Torres, Bioinformatics

Techniques

Dead or Alive? Molecular life-dead distinction in human stool samples reveals significantly different composition of the microbial community – Alexandra Perras, bioRxiv

Critical Assessment of Methods to Quantify Biofilm Growth and Evaluate Antibiofilm Activity of Host Defence Peptides – Evan F. Haney, Biomolecules

June 12, 2018

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Gut and General Microbiome

Screening for Nonalcoholic Fatty Liver Disease in Inflammatory Bowel Diseases: A Cohort Study Using Transient Elastography – Chiara Saroli Palumbo – Inflammatory Bowel Diseases

Review: A critical appraisal of advances in the diagnosis of diverticular disease – Antonio Tursi – Expert Review of Gastroenterology & Hepatology  

Antimicrobial-Induced Cytopenia and Bone Marrow Hypocellularity in Patients with Cirrhosis – Anupama Patil – Bone Marrow Research

Colonic Mucosal Microbiota in Colorectal Cancer: A Single-Center Metagenomic Study in Saudi Arabia – Ahmed O. Alomair – Gastroenterology Research and Practice

Connecting homocysteine and obesity through pyroptosis, gut microbiome, epigenetics, peroxisome proliferator-activator receptor γ (PPARγ) and zinc finger protein 407 (Zfp407) – Anwesha Laha – Canadian Journal of Physiology and Pharmacology

Review: Sexual dimorphism of cardiometabolic dysfunction: Gut microbiome in the play? – Tzu-Wen L. Cross – Molecular Metabolism

Individuality and convergence of the infant gut microbiota during the first year of life – Eric J. de Muinck – Nature Communications

Reconstruction of the bifidobacterial pan-secretome reveals the network of extracellular interactions between bifidobacteria and the infant gut – Gabriele Andrea Lugli – Applied and Environmental Microbiology

Commentary: Beyond Oxalobacter: the gut microbiota and kidney stone formation – Gwen Falony – Gut

Nutritional modulation of the intestinal microbiota: future opportunities for the prevention and treatment of neuroimmune and neuroinflammatory disease – Vincent C.Lombardi – The Journal of Nutritional Biochemistry

 

Reproductive and Urinary Tract Microbiome

Review: Implantation failure of endometrial origin: what is new? –  Jose Bellver – Current Opinion in Obstetrics and Gynecology

Detecting viral genomes in the female urinary microbiome – Andrea Garretto – Journal of General Virology

Commentary: Regional Caesarean Delivery Practices, the Maternal-Infant Microbiome, and Risk for Asthma – Rebecca Entz – Journal of Obstetrics and Gynaecology Canada

 

Skin Microbiome

Insights into the skin microbiome dynamics of leprosy patients during multi-drug therapy and in healthy individuals from Brazil – Paulo E. S. Silva – Scientific Reports

Skin Microbiota in Obese Women at Risk for Surgical Site Infection After Cesarean Delivery – Kara M. Rood – Scientific Reports

 

Oral and Respiratory Microbiome

Analysis of the oral microbiome on the surface of modified dental polymers – Denise Tornavoide Castro – Archives of Oral Biology

Bacterial biogeography of adult airways in atopic asthma – Juliana Durack – Microbiome

Review: Adenotonsillar microbiome: an update – James Jordan Johnston – Postgraduate Medical Journal

 

Animal Microbiome

The canine gut microbiome is associated with higher risk of gastric dilatation-volvulus and high risk genetic variants of the immune system – Meredith A. J. Hullar – PLOS ONE

Propolis from Different Geographic Origins Suppress Intestinal Inflammation in a Model of DSS‐Induced Colitis is Associated with Decreased Bacteroides spp. in the Gut – Kai Wang – Molecular Nutrition & Food Research

Deficiency of BrpA in Streptococcus mutans Reduces Virulence in Rat Caries Model – Zezhang T. Wen – Molecular Oral Microbiology

Huddling remodels gut microbiota to reduce energy requirements in a small mammal species during cold exposure – Xue-Ying Zhang – Microbiome

Abnormal gut microbiota composition contributes to cognitive dysfunction in SAMP8 mice – Gaofeng Zhan – Aging

The role of regulator FucP in Edwardsiella tarda pathogenesis and the inflammatory cytokine response in tilapia – Jiayan Wu – Fish & Shellfish Immunology

Malassezia pachydermatis from animals: Planktonic and biofilm antifungal susceptibility and its virulence arsenal – Raimunda Sâmia Nogueira Brilhante – Veterinary Microbiology

 

Beneficial Microbes

Oral administration of Bifidobacterium bifidum TMC3115 to neonatal mice may alleviate IgE-mediated allergic risk in adulthood – R.Y. Cheng – Beneficial Microbes

Three-Month Feeding Integration With Bifidobacterium Strains Prevents Gastrointestinal Symptoms in Healthy Newborns – Irene Aloisio – Frontiers in Nutrition

 

Bioinformatics and Genomics

Review: Interrogating the microbiome: experimental and computational considerations in support of study reproducibility – Carine Poussin – Drug Discovery Today

CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software – Toby J. Wilkinson – Frontiers in Microbiology

Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity – Andrea Hahn – Frontiers in Microbiology

Next-Generation Machine Learning for Biological Networks – Diogo M. Camacho – Cell

 

May 31, 2018

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Metagenomic analysis of the endangered kakapo fecal microbiota, a role for the microbiota in the social interaction habits of mice, using fecal metabolomics to readout functions of the gut microbiome.

General microbiome

Pre-print: Measuring the archaeome: detection and quantification of archaea signatures in the human body – Manuela R Pausan – bioRxiv

Human skin microbiome

Short‐term direct contact with soil and plant materials leads to an immediate increase in diversity of skin microbiota – Mira Grönroos – Microbiology Open

Human oral microbiome

Preliminary esophageal microbiome studies prompt important scientific questions – Yash Choksi – Clinical and Translational Gastroenterology

Human urinary microbiome

Calcium Oxalate Urolithiasis: A Case of Missing Microbes? – Carlos Alfredo Batagello – Journal of Endourology

Animal experiments

Social interaction-induced activation of RNA splicing in the amygdala of microbiome-deficient mice – Roman M Stilling – eLIFE

Differences in cecal microbiome of selected high and low feather-pecking laying hens – P Birkl – Poultry Science

Digestive microbiota is different in pigs receiving antimicrobials or a feed additive during the nursery period – Cassandra Soler – PLOS ONE

Dietary supplementation with yeast hydrolysate in pregnancy influences colostrum yield and gut microbiota of sows and piglets after birth – Shah Hasah – PLOS ONE

Dietary sodium butyrate improves intestinal development and function by modulating the microbial community in broilers – Wei Wu – PLOS ONE

Animal microbiome

Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo – David W Waite – Scientific Reports

Bacterial diversity and community structure of the intestinal microbiome of Channel Catfish (Ictalurus punctatus) during ontogenesis – Francisca A Burgos – Systematic and Applied Microbiology

Plant, root, and soil microbiome

Pre-print: Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes – Hirokazu Toju – bioRxiv

The importance of phyllosphere on plant functional ecology: a phyllo trait manifesto – Bruno H P Rosado – New Phytologist

Biocatalytic potential of Streptomyces spp. isolates from rhizosphere of plants and mycorrhizosphere of fungi – Jelena Spasic – Biotechnology and Applied Biochemistry

Hosts do not simply outsource pathogen resistance to protective symbionts – Jan Hrček – Evolution

Water and extremophile microbiome

Microbial Diversity in Sediments from the Bottom of the Challenger Deep, the Mariana Trench – Takuro Nunoura – Microbes and Environments

Microbial Community Composition and Putative Biogeochemical Functions in the Sediment and Water of Tropical Granite Quarry Lakes – Amit Kumar – Microbial Ecology

Bloom of a denitrifying methanotroph, “Candidatus Methylomirabilis limnetica”, in a deep stratified lake – Jon S Graf – Environmental Microbiology

Food microbiology

Microbiome dynamics during spontaneous fermentations of sound grapes in comparison with sour rot and Botrytis infected grapes – Jessica Lleixà – International Journal of Food Microbiology

Pre-print: Microbial Community Structure and Diversity of Shrimp Paste at Different Fermentation Stages – Dai Lingying – bioRxiv

Bioinformatics

MetaHMM: A webserver for identifying novel genes with specified functions in metagenomic samples – Balázs Szalkai – Genomics

Metabolomics

The fecal metabolome as a functional readout of the gut microbiome – Jonas Zierer – Nature Genetics

More microbes

Pre-print: Aggregation of Vibrio cholerae by cationic polymers enhances quorum sensing but over-rides biofilm dissipation in response to autoinduction – Nicolas Perez-Soto – bioRxiv

Microbes in the news

Virus genes from city pond rescue bacteria – ScienceDaily