July 23, 2017

General microbiome

Systems biology of lactic acid bacteria: For food and thought – Bas Teusink, Current Opinion in Systems Biology

Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta) – Susan H. Brawley, PNAS

Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions – Nolwenn M. Dheilly, mSystems

Human respiratory microbiome

Airway microbiota signals anabolic and catabolic remodeling in the transplanted lung – Stéphane Mouraux, Journal of Allergy and Clinical Immunology

Human skin microbiome

The Skin Microbiome of Cohabiting Couples – Ashley A. Ross, mSystems

Human oral microbiome

Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules – Anna Edlund, mSystems

Human gut microbiome

Sequencing the gut metagenome as a non-invasive diagnosis for advanced nonalcoholic steatohepatitis – Lixin Zhu, Hepatology

Molecular Characterization of the Human Stomach Microbiota in Gastric Cancer Patients – Guoqin Yu, Frontiers in Microbiology

Inulin-type fructans and whey protein both modulate appetite but only fructans alter gut microbiota in adults with overweight/obesity: a randomized controlled trial – Raylene A. Reimer, Molecular Research and Food Research

Incomplete metabolism of phytoestrogens by gut microbiota from children under the age of three – Pilar Gaya, International Journal of Food Sciences and Nutrition

Animal experiments

An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli – Roderick M. Card, mBio

Maternally-transmitted microbiota affects odor emission and preference in Drosophila larva – Jean-Pierre Farine, Scientific Reports

Burn Injury Leads to Increase in Relative Abundance of Opportunistic Pathogens in the Rat Gastrointestinal Microbiome – Guangtao Huang, Scientific Reports

Linking Sex Differences in Non-Alcoholic Fatty Liver Disease to Bile Acid Signaling, Gut Microbiota, and High Fat Diet  – John Y.L. Chiang, The American Journal of Pathology

Early-life disruption of amphibian microbiota decreases later-life resistance to parasites – Sarah A. Knutie, Nature Communication

In vitro characteristics of an Atlantic salmon (Salmo salar L.) hind gut microbial community in relation to different dietary treatments – Kamarul Zaman Zarkasia,  Research in Microbiology

Effects of coconut oil on glycemia, inflammation, and urogenital microbial parameters in female Ossabaw mini-pigs – Annie E. Newell-Fugate, PLoS ONE

Effect of acute ozone exposure on the lung metabolomes of obese and lean mice – Joel Andrew Mathews, PLoS ONE

Animal microbiome

Skin Bacterial Community Reorganization Following Metamorphosis of the Fire-Bellied Toad (Bombina orientalis) – Arnaud Bataille, Microbial Ecology

Inferring microbial interactions in thermophilic and mesophilic anaerobic digestion of hog waste – Grace Tzun-Wen Shaw, PLoS ONE

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation – Olov Svartström, ISME

Genome Sequences of Two Shewanella spp. Isolated from the Gut of the Sea Cucumber Apostichopus japonicus (Selenka, 1867) – Hyun-Hee Hong, Genome Anouncements

Feather-Degrading Bacteria: Their Biochemical and Genetic Characteristics – Paweł Kowalczyk, Arabian Journal for Science and Engineering

Plant, root, and soil microbiome

The tree species matters: Belowground carbon input and utilization in the myco-rhizosphere – Janine Sommera, European Journal of Soil Biology

Soil bacterial community response to vegetation succession after fencing in the grassland of China – Quanchao Zeng, Science of The Total Environment

Drought Stress Results in a Compartment-Specific Restructuring of the Rice Root-Associated Microbiomes – Christian Santos-Medellín, mBio

Improved grain yield of cowpea (Vigna unguiculata) under water deficit after inoculation with Bradyrhizobium elkaniiand Rhizophagus irregularis – Rui S. Oliveira, Crop and Pasture Science

Understanding the holobiont: the interdependence of plants and their microbiome – Carmen Sánchez-Cañizares, Current Opinion in Microbiology

Pseudomonas fluorescens R68 assisted enhancement in growth and fertilizer utilization of Amaranthus tricolor (L.) – C. Jimtha John, 3Biotech

Ecological guild and enzyme activities of rhizosphere soil microbial communities associated with Bt-maize cultivation under field conditions in North West Province of South Africa – Deidré A. B. van Wyk, Journal of Basic Microbiology

A genomic perspective on stoichiometric regulation of soil carbon cycling – Wyatt H Hartman, ISME

The rhizosphere microbiome of burned holm-oak: potential role of the genus Arthrobacter in the recovery of burned soils – Antonio J. Fernández-González, Scientific Reports

The tree species matters: Belowground carbon input and utilization in the myco-rhizosphere – Janine Sommera, European Journal of Soil Biology

Biological control of potential antagonistic bacteria isolates to restrict Magnaporthe grisea infection on rice – David P. Tokpah, African Journal of Microbiology Research

Bacteria associated to plants naturally selected in a historical PCB polluted soil show potential to sustain natural attenuation – Lorenzo Vergani, Frontiers in Microbiology

Water and extremophile microbiome

Unraveling the Microbial Interactions and Metabolic Potentials in Pre- and Post-treated Sludge from a Wastewater Treatment Plant Using Metagenomic Studies – Chandni Sidhu, Frontiers in Microbiology

Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China – Jian-Qiang Su, Microbiome

Microbial Community Structure and Function Decoupling Across a Phosphorus Gradient in Streams – Erick S. LeBrun, Microbial Ecology

Microbial communities and their predicted metabolic functions in growth laminae of a unique large conical mat from Lake Untersee, East Antarctica – Hyunmin Koo, Frontiers in Microbiology

Draft genome sequence of Exiguobacterium aurantiacumstrain PN47 isolate from saline ponds, known as “Salar del Huasco”, located in the Altiplano in the North of Chile – Erwin Strahsburger, Brazilian Journal of Microbiology

Diversity of culturable filamentous Ascomycetes in the eastern South Pacific Ocean off Chile – Jeanett Vera, World Journal of Microbiology and Biotechnology

Salinity Drives the Virioplankton Abundance but Not Production in Tropical Coastal Lagoons – Pedro C. Junger, Microbial Ecology

Characterization of a cold-adapted DNA photolyase from C. psychrerythraea 34H – Sudipto Munshi, Extremophiles

Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor – Alma E Parada, ISME

Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars – Shino Suzuki, ISME

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept – Melissa B. Duhaime, Frontier in Microbiology

Effects of Physiochemical Factors on Prokaryotic Biodiversity in Malaysian Circumneutral Hot Springs – Chia S. Chan, Frontiers in Microbiology

Climate oscillations reflected within the microbiome of Arabian Sea sediments – William D. Orsi, Scientific Reports

Microbiome of Trichodesmium Colonies from the North Pacific Subtropical Gyre – Mary R. Gradoville, Frontiers in Microbiology

Antarctic sea ice region as a source of biogenic organic nitrogen in aerosols – Manuel Dall’Osto, Scientific Reports

Built environment

A role for microbial selection in frescoes’ deterioration in Tomba degli Scudi in Tarquinia, Italy – Maria Cristina Tomassetti, Scientific Reports

Food microbiology

An Exploration into the Bacterial Community under Different Pasteurization Conditions during Substrate Preparation (Composting–Phase II) for Agaricus bisporus Cultivation – Fabricio Rocha Vieira, Microbial Ecology

Metagenome-based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments – Conor J Doyle, Environmental Microbiology

Draft Genome Sequences of Three Lactobacillusparacasei Strains, Members of the Nonstarter Microbiota of Mature Cheddar Cheese – Ewelina Stefanovic, Genome Anouncements

Bioinformatics

Cohesion: a method for quantifying the connectivity of microbial communities – Cristina M Herren, ISME

Developing integrative systematics in the informatics and genomic era, and calling for a global Biodiversity Cyberbank – Jun Wen, Journal of Systematics and Evolution

Techniques

Rapid differentiation of bacterial communities using high resolution melting analysis – Steven Everman, Journal of Microbiological Methods

Proteomics in Inflammatory Bowel Disease: Approach Using Animal Models – Fadi H. Mourad, Digestive Diseases and Sciences

17, July 2017

In today’s digest, we learn more about how cloud-based computing is making it easier to analyses big datasets, and stochastic bottlenecks control bacterial colonization in animal host.

General Microbiome and Microbiology

New perspectives on dandruff and seborrheic dermatitis: lessons we learned from bacterial and fungal skin microbiota.

Paulino LC. European journal of dermatology

Harnessing microbiome‐based biotechnologies for sustainable mitigation of nitrous oxide emissions

Hu HW.Microbial Biotechnology

Human gut microbiome

Comparisons of Gut Microbiota Among Healthy Control, Patients With Conventional Adenoma, Sessile Serrated Adenoma, and Colorectal Cancer. Yoon H. Journal of Cancer Prevention

Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life. Xiong W. Microbiome

Assessing the impact of protein extraction methods for human gut metaproteomics

Zhang  X.Journal of Proteomics

Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls

Stewart CJ. Microbiome

Animal and insect microbiome

Host–Microbe Interactions: Winning the Colonization Lottery

Lazzaro BP and GM Fox. Current Biology

Strategies for managing rival bacterial communities: lessons from burying beetles.

Kilner RM. Journal of Animal Ecology

Changes in the Gut Microbial Communities Following Addition of Walnuts to the Diet. Byerley, LO. Journal of Nutritional Biochemistry

Microbiome modelling

The Microbiome and Big Data

Navas-Molina JA. Current Opinion in Systems Biology

Plant, soil, and air microbiome

Differences in soil biological activity by terrain types at the sub-field scale in central Iowa US.

Kaleita AL.PloS one

Intercropping affects genetic potential for inorganic nitrogen cycling by root-associated microorganisms in Medicago sativa and Dactylis glomerata

Zhao M. Applied Soil Ecology

Changes in microbial community composition following phytostabilization of an extremely acidic Cu mine tailings

Yang T. Soil Biology and Biochemistry

Effects of between‐site variation in soil microbial communities and plant‐soil feedbacks on the productivity and composition of plant communities.   Bauer JT.Journal of Applied Ecology

Response of soil microbial communities to elevated antimony and arsenic contamination indicates the relationship between the innate microbiota and contaminant fractions. Sun W. Environmental Science and Technology

Marine and inland waters

The contribution of microbial biotechnology to mitigating coral reef degradation Damjanovic. Microbial Biotechnology

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

Slaby BM. The ISME Journal

Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions

He T.  mBio

Built Microbiome

Microbial communities on painted wet and dry external surfaces of a historic fortress in Niterói, Brazil. Ogawa A. Journal of International Biodeterioration & Biodegradation

Preprint

Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity.Gerth M.PeerJ

July 6, 2017

The microbiota of spotted hyenas, a review of potential interactions between olfactory sensation and the microbiome-gut-brain axis, phylogenetic analysis of host-microbe symbioses to examine the evolution of dependence over time.

General microbiome

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia – Sami Ben Said – Frontiers in Microbiology

The evolution of host-symbiont dependence – Roberta M Fisher – Nature Communications

Review: The microbiota revolution: Excitement and caution – Maria Rescigno – European Journal of Immunology

Review: The Microbiome and Blood Pressure: Can Microbes Regulate Our Blood Pressure? – Souhaila Al Khodor – Frontiers in Pediatrics

Human oral microbiome

Suppression of αvβ6 Integrin Expression by Polymicrobial Oral Biofilms in Gingival Epithelial Cells – Jiarui Bi – Scientific Reports

Proteomic shifts in multi-species oral biofilms caused by Anaeroglobus geminatus – Kai Bao – Scientific Reports

Human vaginal microbiome

Quantifying the human vaginal community state types (CSTs) with the species specificity index – Zhanshan Ma – PeerJ

Animal experiments

Effects of iron supplementation on growth, gut microbiota, metabolomics and cognitive development of rat pups – Erica E Alexeev – PLOS ONE

Review: Disruptive physiology: olfaction and the microbiome-gut-brain axis – John Bienenstock – Biological Reviews Cambridge Philosophical Society

Effects of melanin from Sepiella Maindroni ink (MSMI) on the intestinal Microbiome of mice – Hui Dong – BMC Microbiology

Animal microbiome

The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition – Emanuel Heitlinger – Frontiers in Cellular and Infection Microbiology

Plant, root, and soil microbiome

Perspective: The deep, hot biosphere: Twenty-five years of retrospection – Daniel R Colman – PNAS

Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus “Hitchhiker” from the Soybean Rhizosphere – Gabriel L Lozano – Genome Announcements

Warmer winters increase the rhizosphere carbon flow to mycorrhizal fungi more than to other microorganisms in a temperate grassland – Johanna Birgander – Global Change Biology

Negative plant-phyllosphere feedbacks in native Asteraceae hosts – a novel extension of the plant-soil feedback framework – Briana K Whitaker – Ecology Letters

Water and extremophile microbiome

Size and composition of subseafloor microbial community in the Benguela upwelling area examined from intact membrane lipid and DNA analysis – Thomas W Evans – Organic Geochemistry

FurukawaMarine microbes as a valuable resource for brand new industrial biocatalysts – Azadeh Beygmoradi – Biocatalysts and Agricultural Biotechnology

Antagonistic Interactions and Biofilm Forming Capabilities Among Bacterial Strains Isolated from the Egg Surfaces of Lake Sturgeon (Acipenser fulvescens) – M Fujimoto – Microbial Ecology

Probiotics/prebiotics

Effects of the probiotic Bifidobacterium animalis subsp. lactis on the non-surgical treatment of periodontitis. A histomorphometric, microtomographic and immunohistochemical study in rats – Milla S T Ricoldi – PLOS ONE

Phages and viruses

Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics – Mohammad Moniruzzaman – Nature Communications

Occurrence of Bacillus thuringensis Bacteriophages in the Egyptian Arid Soil – Amel S M Abo-Senna – International Journal of Virology and Molecular Biology

Bioinformatics

A conceptual framework for quality assessment and management of biodiversity data – Allan Koch Veiga – PLOS ONE

Techniques

SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures – Joost Willemse – bioRxiv

Mapping-based all-RNA-information sequencing analysis (ARIseq) pipeline simultaneously revealed taxonomic composition, gene expression, and their correlation in an acidic stream ecosystem – Arisa Tsuboi – bioRxiv

More microbes

Review: Metabolic engineering pathways for rare sugars biosynthesis, physiological functionalities, and applications – A review – Muhammad Bilal – Critical Reviews in Food Science and Nutrition

Microbes in the news

Microbes aren’t the enemy, they’re a big part of who we are – Amy Loughman – Medical Xpress

What Cheese Can Tell Us About Antibiotic Resistance – Jason Tetro – Huffington Post Canada

Cases of recurrent Clostridium difficile infection are soaring – Medical Xpress

Helium ions reveal how viruses attack bacteria – ScienceDaily

April 5, 2017

Today’s digest features interesting research on the dynamic microbiome evolution in social bees and the alteration in quorum Sensing, cell motility, stress Response, and carbohydrate metabolism  of gut microbiome by the organophosphate pesticide Diazinon. Low dose penicillin in early life can induce long term changes in mice gut microbiota, brain cytokines and behavior. Interesting reviews on the microbiome and human biology, and role of gut microbiota in the development of hypertension, including that associated with obstructive sleep apnea.

General microbiome

*Review: The Microbiome and Human Biology – Rob Knight – Annual Review of Genomics and Human Genetics

*Dynamic microbiome evolution in social bees – Waldan K. Kwong – Science Advances

Anaerobic Bacterial Fermentation Products Increase Tuberculosis Risk in Antiretroviral-Drug-Treated HIV – Leopoldo N. Segal – Cell Host & Microbe

Pregnancy and early life

Vancomycin treatment is a risk factor for vancomycin-nonsusceptible Staphylococcus capitis sepsis in preterm neonates – Marine Butin – Clinical Microbiology and Infection

Human oral microbiome

Relative abundance of total subgingival plaque-specific bacteria in salivary microbiota reflects the overall periodontal condition in patients with periodontitis – Shinya Kageyama – Plos One

Review: Biofilm over teeth and restorations: What do we need to know? – Nancy J. Lin – Dental Materials

Human skin microbiome

Cutaneous Burn Injury Promotes Shifts in the Bacterial Microbiome in Autologous Donor Skin: Implications for Skin Grafting Outcomes – Jennifer K. Plichta – Shock

Human gut microbiome

Review : The gut microbiota: a possible factor influencing systemic lupus erythematosus – Hadar Neuman – Current Opinion in Rheumatology

*Organophosphate Diazinon Altered Quorum Sensing, Cell Motility, Stress Response, and Carbohydrate Metabolism of Gut Microbiome – Bei Gao -Toxicological Sciences

Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab – N. Chaput – Oncology

*Review: Obstructive Sleep Apnea-Induced Hypertension: Role of the Gut Microbiota – David J. Durgan – Current Hypertension Reports

Review: The Gut Microbiota and Alzheimer’s Disease – Chunmei Jiang – Journal of Alzheimer’s Disease

Fecal Microbiota Transplantation

Fecal Microbiota Transplantation in Patients with Blood Disorders Inhibits Gut Colonization with Antibiotic-Resistant Bacteria: Results of a Prospective, Single-Center Study – Jaroslaw Bilinski – Clinical Infectious Diseases

Animal microbiome

Multi-Omics Analysis Reveals a Correlation between the Host Phylogeny, Gut Microbiota and Metabolite Profiles in Cyprinid Fishes – Tongtong Li – Frontiers in Microbiology

Diurnal Dynamics of Gaseous and Dissolved Metabolites and Microbiota Composition in the Bovine Rumen – Henk J. van Lingen – Frontiers in Microbiology

Microbial Biogeography and Core Microbiota of the Rat Digestive Tract – Dongyao Li – Scientific Reports

Animal experiments

Bifidobacterium in the gut microbiota confer resilience to chronic social defeat stress in mice – Chun Yang – Scientific Reports

Lack of Evidence That Selenium-Yeast Improves Chicken Health and Modulates the Caecal Microbiota in the Context of Colonization by Campylobacter jejuni – Alexandre Thibodeau – Frontiers in Microbiology

Review : Outstanding animal studies in allergy II: from atopic barrier and microbiome to allergen-specific immunotherapy – Erika Jensen-Jarolim – Current Opinion in Allergy & Clinical Immunology

Faecalibacterium prausnitzii treatment improves hepatic health and reduces adipose tissue inflammation in high-fat fed mice – Eveliina Munukka – ISME Journal

*Low-dose penicillin in early life induces long-term changes in murine gut microbiota, brain cytokines and behavior –  Sophie Leclercq – Nature Communications

Nod2 and Nod2-regulated microbiota protect BALB/c mice from diet-induced obesity and metabolic dysfunction – Ivan Rodriguez-Nunez – Scientific Reports

Plant, root, and soil microbiome

Aluminum-tolerant bacteria improve the plant growth and phosphorus content in ryegrass grown in a volcanic soil amended with cattle dung manure – María de la Luz Mora- Applied Soil Ecology

Invisible but consequential: root endophytic fungi have variable effects on belowground plant–insect interactions – Huyijuie Gan – Ecosphere

Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China – Qin Tian – Scientific Reports

Phylogenetic conservation of substrate use specialization in leaf litter bacteria – Kristin L. Dolan – Plos ONE

Root biomass and exudates link plant diversity with soil bacterial and fungal biomass – Nico Eisenhauer – Scientific Reports

Water and extremophile microbiome

Discrimination of Four Marine Biofilm-Forming Bacteria by LC-MS Metabolomics and Influence of Culture Parameters – Laurie Favre – Journal of Proteome Research

Iron assimilation and utilization in anaerobic ammonium oxidizing bacteria – Christina Ferousi – Current Opinion in Chemical Biology

*Potential sources of bacteria colonizing the cryoconite of an Alpine glacier – Andrea Franzetti – PLOS ONE

Spatio-Temporal Variations of Marine Biofilm Communities Colonizing Artificial Substrata Including Antifouling Coatings in Contrasted French Coastal Environments – Jean-François Briand – Microbial Ecology

Metabolomics

Review: Metabolomics: Strategies to Define the Role of Metabolism in Virus Infection and Pathogenesis – Marianne Manchester – Advances in Virus Research

Effect of Major Royal Jelly Proteins on Spatial Memory in Aged Rats: Metabolomics Analysis in Urine – Di Chen -Journal of Agricultural and Food Chemistry

Food microbiology

Sourdough authentication: quantitative PCR to detect the lactic acid bacterial microbiota in breads – Erica Pontonio – Scientific Reports

Probiotics / prebiotics

Evaluation of Potential Probiotics Isolated from Human Milk and Colostrum – Quésia S. Damaceno – Probiotics and Antimicrobial Proteins

Bioinformatics

SLIMM: species level identification of microorganisms from metagenomes – Temesgen Hailemariam Dadi – PeerJ

Techniques

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area – Kazuma Nakano – Human Cell

High-pressure microscopy for tracking dynamic properties of molecular machines – Masayoshi Nishiyama – Biophysical Chemistry

Gut Microbiome Standardization in Control and Experimental Mice – Kathy D. McCoy – Current Protocols in Immunology

Diastereomer-specific Quantification of Bioactive Hexosylceramides from Bacteria and Mammals – Johanna von Gerichten – Journal of Lipid Research

Microbes in the news

Genetically engineered microbes make their own fertilizer, could feed the world’s poorest

The Next Plague (5) Bacteria: The Coming And Going And Coming Again Of Bacterial Plagues

Latest Helicobacter pylori breakthrough could lead to eradication of bacteria

Science, publishing, and career

Journal editor calls for ‘culture change’ around clinical trial data

Anitha’s non-microbiology picks

In the quest of Planet 9

March 11, 2017

General microbiome

Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis – M Pammi – Microbiome

Is the 25 year hepatitis C marathon coming to an end to declare victory? – Khulood T Ahmed – bioRxiv

Natural antimicrobial peptide complexes in the fighting of antibiotic resistant biofilms: Calliphora vicina medicinal maggots – N Gordya – PLoS One

Complement inhibition by Sarcoptes scabiei protects Streptococcus pyogenes – An in vitro study to unravel the molecular mechanisms behind the poorly understood predilection of S. pyogenes to infect mite-induced skin lesions – PM Swe – PLoS Neglected Tropical Disease

CD40-signalling abrogates induction of RORγt+ Treg cells by intestinal CD103+ DCs and causes fatal colitis – C Barthels – Nature Communications

Antioxidant Supplements and Gastrointestinal Diseases: A Critical Appraisal – I Khan – Medical Principles and Practice

 

Human skin microbiome

Prenatal antibiotics and atopic dermatitis among 18-month old children in the Danish National Birth Cohort – S Timm – Clinical and Experimental Allergy

 

Human vaginal microbiome

*Review: Vaginal Microbiome and Its Relationship to Behavior, Sexual Health, and Sexually Transmitted Diseases – FM Lewis – Obstetrics and Gynecology

 

Human gut microbiome

*Review: Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome: A Bridge between Functional Organic Dichotomy – UC Ghoshal – Gut and Liver

Beyond Digestion: The Pancreas Shapes Intestinal Microbiota and Immunity – H Tilg – Cell Metabolism

Melatonin prevents obesity through modulation of gut microbiota in mice – P Xu – Journal of Pineal Research

 

Animal microbiome

Dynamic changes of the respiratory microbiota and its relationship to fecal and blood microbiota in healthy young cats – Vientós-Plotts AI – PLoS One

A gut reaction: The combined influence of exercise and diet on gastrointestinal microbiota in rats – R Batacan – Journal of Applied Microbiology

Parasitism perturbs the mucosal microbiome of Atlantic Salmon – MS Llewellyn – Scientific Reports

Probiotic efficiency of Bacillus sp. in Labeo rohita challenged by Aeromonas hydrophila: assessment of stress profile, haemato-biochemical parameters and immune responses – A Nandi – Aquaculture Research

 

Plant, root and soil microbiome

Simplified and representative bacterial community of maize roots – B Niu – PNAS

Impact of three different fungicides on fungal epi- and endophytic communities of common bean (Phaseolus vulgaris) and broad bean (Vicia faba) – R Prior – Journal of Environmental Science and Health, Part B

Thermophilic microorganisms in arable land around medieval archaeological sites in Northern Caucasus, Russia: Novel evidence of past manuring practices – E Chernysheva – Geoarchaeology

 

Water and Extremophiles

In situ electrochemical enrichment and isolation of a magnetite-reducing bacterium from a high pH serpentinizing spring – AR Rowe – Environmental Microbiology

Niche specialization of bacteria in permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica – M Kwon – Environmental Microbiology

 

Transcriptomics and Proteomics

A Comprehensive Assessment of the Genetic Determinants in Salmonella Typhimurium for Resistance to Hydrogen Peroxide – Sardar Karash – bioRxiv

 

Techniques

Isolation and concentration of bacteria from blood using microfluidic membraneless dialysis and dielectrophoresis – L D’Amico – Lab on a Chip

A fast small-sample kernel independence test for microbiome community-level association analysis – X Zhan – Biometrics

 

More microbes

Integrative Physiology: At the Crossroads of Nutrition, Microbiota, Animal Physiology, and Human Health – Leulier F – Cell Metabolism

Phage therapy is highly effective against chronic lung infections with Pseudomonas aeruginosa – EM Waters – Thorax

*Review: Recent advances in genetic modification systems for Actinobacteria – Yu Deng – Applied Microbiology and Biotechnology

Meibomian gland disease and the microbiotome: is it time for ocular probiotics? – S Watson – Clinical & Experimental Ophthalmology

*ReviewInfection in Organ Transplantation – JA Fishman – American Journal of Transplantation

Azole resistance in Candida albicans from animals: Highlights on efflux pump activity and gene overexpression – MFG Rocha – Mycoses

The Synonymy of the Toxic Dinoflagellates Prorocentrum mexicanum and P. rhathymum and the Description of P. steidingerae sp. nov. (Prorocentrales, Dinophyceae) – F Gomez – Journal of Eukaryotic Microbiology

Gut microbiota analysis in rats with methamphetamine-induced conditioned place preference – T Ning – bioRxiv

 

Microbes in news

What is Metagenomics? – Y Smith – News Medical

UCC researchers discover weapon to fight antibiotic resistance – D Ahlstrom – The Irish Times

Community gets an eye-opening lesson in human microbiome and our western lifestyle – C MacDonald – UToday

Microbiome Research Symposia Review: Microbiome and Diseases – J Phelan – Taconic Biosciences

Q&A with Zeus Capital’s Dr Gary Waanders: Live Biotherapeutics & 4D Pharma PLC (LON:DDDD) – A Stone – Directors Talk Interviews

Do You Have the Guts to Perform? Microbial Balance, the Brain and Athletic Performance – SJ Hewlings – Natural Products Insider

New probiotics meant to balance microbial, fungal communities in gut – H Schultz – NUTRAingredients

Google Leads $51M Investment in Startup Tackling Drug-Resistant Bacteria – R Bushey – R & D

Your bacteria-ridden makeup could be the reason you keep getting sick – A Mulvaney – Independent

February 25, 2017

Insight into the role of gut microbiome lipid metabolites in central nervous system diseases. A role of invasive plants in altering the soil microbiome. Evidence that microbiome alterations in Crohn’s disease are not genetically based.

Events and jobs

Post-Doctoral Research Associate in immunology, microbiology, virology, and/or biochemistry – MRIGlobal, Gaithersburg, Maryland, USA

Research Scientist – Department of Microbiology – University of Illinois at Urbana-Champaign, USA

Part-Time Microbiology Instructor – Foothill-De Anza Community College District, California, USA

First Stage Researcher with background in environmental microbiology – Faculty of Biology, University of Warsaw, Poland

General microbiome

Altered antibiotic tolerance in anaerobic digesters acclimated to triclosan or triclocarban – Daniel E. Carey – Chemosphere

Antimicrobial Resistance and Molecular Characterization of Extended-Spectrum β-Lactamases and Other Escherichia coli Isolated from Food of Animal Origin and Human Intestinal Isolates – Krizman M – Journal of Food Protection

Human oral microbiome

Prospective, randomised, controlled study evaluating early modification of oral microbiota following admission to the intensive care unit and oral hygiene with chlorhexidine – Felipe Francisco Tuon – Journal of Global Antimicrobial Resistance

The potential effect of oral microbiota in the prediction of mucositis during radiotherapy for nasopharyngeal carcinoma -Xiao-Xia Zhu – EBioMedicine

Human urinary microbiome

*Special Issue Preface: Preface to the human microbiome in urologic health and disease – Daniel A. Shoskes – Annals of Translational Medicine

*Review: The mycobiome of the human urinary tract: potential roles for fungi in urology – A. Lenore Ackerman – Annals of Translational Medicine

Human vaginal microbiome

Longitudinal analysis of vaginal microbiota in women with recurrent vulvovaginal candidiasis – Ma X – Journal of Southern Medical University (Nan Fang Yi Ke Da Xue Xue Bao)

Human gut microbiome

The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred – Umer Zeeshan Ijaz – PLOS

Randomised clinical trial: faecal microbiota transplantation for recurrent Clostridum difficile infection – fresh, or frozen, or lyophilised microbiota from a small pool of healthy donors delivered by colonoscopy – Z.D Jiang – Alimentary Pharmacology and Therapeutics

Gut-brain axis: Role of lipids in the regulation of inflammation, pain and CNS diseases – Russo R – Current Medicinal Chemistry

What roles do colon stem cells and gap junctions play in the left and right location of origin of colorectal cancers? – James E. Trosko – Journal of Cell Communication and Signaling

Contributions of the Interaction between Dietary Protein and Gut Microbiota to Intestinal Health – Ma N – Current Protein and Peptide Science

*Review: Dietary Fiber Gap and Host Gut Microbiota – Han M – Protein Peptide Letters

Structural Modulation of Gut Microbiota during Alleviation of Antibiotic-Associated Diarrhea with Herbal Formula – Weijie Lv – International Journal of Biological Macromolecules

Association of diverse bacterial communities in human bile samples with biliary tract disorders: a survey using culture and polymerase chain reaction-denaturing gradient gel electrophoresis methods – E. Tajeddin – European Journal of Clinical Microbiology & Infectious Disease

Immunomodulatory Effects of Lactobacillus plantarumLp62 on Intestinal Epithelial and Mononuclear Cells – Thalis Ferreira dos Santos – BioMed Research International

How to modulate gut microbiota: diet, pre-probiotics or antibiotics? – Ponziani FR – Minerva Gastroenterologica E Dietologica

* Review: AISF position paper on nonalcoholic fatty liver disease (NAFLD): Updates and future directions – Italian Association for the Study of the Liver (AISF), Lonardo A – Digestive and Liver Disease

Clostridium difficile infection in acute flares of inflammatory bowel disease: A prospective study -Harry Sokol – Digestive and Liver Disease

 Multi-site human microbiome

Porphyromonas gingivalis lipopolysaccharide induces pro-inflammatory adipokine secretion and oxidative stress by regulating Toll-like receptor-mediated signaling pathways and redox enzymes in adipocytes – Fanny Le Sage – Molecular and Cellular Endocrinology

Animal experiments

Impact of TIGECYCLINE versus other antibiotics on the fecal metabolome and on colonization resistance to CLOSTRIDIUM DIFFICILE in mice – Robin L.P. Jump – Pathological Immunology

Animal microbiome

Temporal Stability and the Effect of Transgenerational Transfer on Fecal Microbiota Structure in a Long Distance Migratory Bird – Jakub Kreisinger – Frontiers in Microbology

Convergent patterns in the evolution of mealybug symbioses involving different intrabacterial symbionts – Gitta Szabó – The ISME Journal

New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11 – Lindsey M Solden – The ISME Journal

Changes in rumen microbiota composition and in situ degradation kinetics during the dry period and early lactation as affected by rate of increase of concentrate allowance – K. Dieho – Journal of Dairy Science

Plant, root, and soil microbiome

Response of rhizosphere soil microbial to Deyeuxia angustifolia encroaching in two different vegetation communities in alpine tundra – Lin Li – Scientific Reports

Influence of phylogenetic conservatism and trait convergence on the interactions between fungal root endophytes and plants – Sevda Haghi Kia – The ISME Journal

Comparative fibre-degrading capacity in foals at immediate and late post-weaning periods – C. Faubladier – Cambridge Core

The effect of the source of microorganisms on adaptation of hydrolytic consortia dedicated to anaerobic digestion of maize silage – Krzysztof Poszytek – Anaerobe

Water and extremophile microbiome

Diversity of crude oil-degrading bacteria and alkane hydroxylase (alkB) genes from the Qinghai-Tibet Plateau – Haozhi Long – Environmental Monitoring and Assessment

Direct single-cell biomass estimates for marine bacteria via Archimedes’ principle – Nathan Cermak – The ISME Journal

Evidence for a role of viruses in the thermal sensitivity of coral photosymbionts – Rachel Ashley Levin – The ISME Journal

Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton – Ryan W Paerl – The ISME Journal

Elevated temperature increases carbon and nitrogen fluxes between phytoplankton and heterotrophic bacteria through physical attachment – Nestor Arandia-Gorostidi – The ISME Journal

Warming and nutrient enrichment in combination increase stochasticity and beta diversity of bacterioplankton assemblages across freshwater mesocosms – Lijuan Ren – The ISME Journal

Integration of Metagenomic and Stable Carbon Isotope Evidence Reveals the Extent and Mechanisms of Carbon Dioxide Fixation in High-Temperature Microbial Communities – Ryan de Montmollin Jennings – Frontiers in Microbiology

Seasonal Variation in Abundance and Diversity of Bacterial Methanotrophs in Five Temperate Lakes – Md Sainur Samad – Frontiers in Microbiology

Predominance of Viable Spore-Forming Piezophilic Bacteria in High-Pressure Enrichment Cultures from ~1.5 to 2.4 km-Deep Coal-Bearing Sediments below the Ocean Floor – Jiasong Fang – Frontiers in Microbiology

Metagenomics and resistome

Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection – Li-Guan Li – The ISME

Metabolomics

Assessment of the bimodality in the distribution of bacterial genome sizes – Hyun S Gweon – The ISME Journal

Genome of ‘Ca. Desulfovibrio trichonymphae’, an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut – Hirokazu Kuwahara – The ISME Journal

A family of interaction-adjusted indices of community similarity – Thomas Sebastian Benedikt Schmidt – The ISME Journal

Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates – Po-Hsiang Wang – The ISME Journal

Phylogenetic relationships among Staphylococcus aureus isolated from clinical samples in Mashhad, Iran – Farzad Khadem – Journal of Infection and Public Health

Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk-disease complex – Abraham Morales-Cruz – Molecular Plant Pathology

More microbes

Redox potential as a master variable controlling pathways of metal reduction by Geobacter sulfurreducens – Caleb E Levar – The ISME Journal

Coupled molecular and isotopic evidence for denitrifier controls over terrestrial nitrogen availability – Erin F E Lennon – The ISME Journal

Enhanced microbial electrosynthesis by using defined co-cultures – Jörg S Deutzmann – The ISME Journal

Temperature is a key factor in Micromonas–virus interactions – David Demory – The ISME Journal

Evolutionary convergence in experimental Pseudomonas populations – Peter A Lind – The ISME Journal

Microbes in the news

Are There Health Benefits To Exposing Our Immune Systems To Bacteria? – Forbes
Nutrition: Trust your gut instincts — whole grains are good for you – Los Angeles Daily News

There could be a surprising link between how people respond to a new cancer treatment and their microbiome – Lydia Ramsey – Business Insider

January 14, 2017

So it is technically already January 15 most countries, but I have been busy today preparing to transfer Microbiome Digest to an eager group of 20 new contributors. It takes a lot of time to hopefully be able to safe some time – if that makes sense.

My inbox is still full of new alerts, but here is what I have been able to “digest” so far. It’s already a lot!

General human microbiome

Navigating social and ethical challenges of biobanking for human microbiome research –
Kim H. Chuong – BMC Medical Ethics

Editorial: Influence of the microbiota on host physiology – moving beyond the gut
– Kim E. Barrett – The Journal of Physiology

Pregnancy and early life

* Pregnant women carrying microcephaly foetuses and Zika virus contain potentially pathogenic microbes and parasites in their amniotic fluid – Diogo Antonio Tschoeke – BMC Medical Genomics

Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota – Jasmine C. C. Davis – Scientific Reports

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates – Matthew R Olm – Genome Research

The Microbiome and Complement Activation A Mechanistic Model for Preterm Birth – Alexis B. Dunn – Biological Research for Nursing

Review: Asthma and the microbiome: defining the critical window in early life – Leah T. Stiemsma – Allergy, Asthma & Clinical Immunology

Human gut microbiome

Alcohol, microbiome, life style influence alcohol and non-alcoholic organ damage – Manuela G. Neuman – Experimental and Molecular Pathology

Serum Trimethylamine N-oxide, Carnitine, Choline and Betaine in Relation to Colorectal Cancer Risk in the Alpha Tocopherol and Beta Carotene Study – Kristin A. Guertin – Cancer Epidemiology, Biomarkers & Prevention

Laboratory Testing of Donors and Stool for Fecal Microbiota Transplantation for Recurrent C. difficile Infection – Michael H. Woodwort – Journal of Clinical Microbiology

Editorial: Gut microbiota: implications for sports and exercise medicine – Owen Cronin – British Journal of Sports Medicine

Review/Addendum: Pathogen control at the intestinal mucosa – H2O2 to the rescue
Ulla G. Knaus – Gut Microbes

Editorial: Tune into the rhythm of your bugs – Purna Kashyap – Science Translational Medicine

Preview: Are Gut Microbes Responsible for Post-dieting Weight Rebound? – Julien Chilloux – Cell Metabolism

Review: Involvement of Reduced Microbial Diversity in Inflammatory Bowel Disease – Dawei Gong – Gastroenterology Research and Practice

Year in Review: Gut microbiota in 2016: A banner year for gut microbiota research – Wendy S. Garrett – Nature Reviews Gastroenterology & Hepatology

Review: Gut microbiota disturbance during helminth infection: can it affect cognition and behaviour of children? – Vanina Guernier – BMC Infectious Diseases

Review: An expanding stage for commensal microbes in host immune regulation – Yan Shi – Cellular & Molecular Immunology

Perspective: Decoding host–microbiota communication in the gut – now we’re flying!
– Stephen J. Keely – The Journal of Physiology

Just based on the abstract, this appears a wild hypothesis potentially ignoring economic status, fiber consumption etc:  Latitude as a co-driver of human gut microbial diversity? – Emma Dikongué – Ideas that Push the Boundaries

Book: Gut Microbiome and Behavior, Volume 131 – John F. Cryan, Gerard Clarke – Elsevier

Animal experiments

Intestinal microbiota as a tetrahydrobiopterin exogenous source in hph-1 mice – Jaques Belik – Scientific Reports

Oral treatment with Lactobacillus rhamnosus attenuates behavioural deficits and immune changes in chronic social stress – Aadil Bharwani – BMC Medicine

Year in review: Microbiome in 2016: T follicular helper cells and the gut microbiome in arthritis – Veena Taneja – Nature Reviews Rheumatology

Animal microbiome

Bacterial Communities Associated with Houseflies (Musca domestica L.) Sampled within and between Farms – Simon Bahrndorff – PLOS ONE

Microbiome variation in corals with distinct depth distribution ranges across a shallow–mesophotic gradient (15–85 m) – Bettina Glasl – Coral Reefs

Symbiont-induced odorant binding proteins mediate insect host hematopoiesis – Joshua B Benoit – eLIFE

Drivers of variation in species impacts for a multi-host fungal disease of bats  –
Kate E. Langwig – Philosophical Transactions of the Royal Society B

Sponges: Evaluating the core microbiota in complex communities: A systematic investigation – Carmen Astudillo-Garcia – Environmental Microbiology

Plant, root, and soil microbiome

Bacterial community composition in costal dunes of the Mediterranean along a gradient from the sea shore to the inland – Haggai Wasserstrom – Scientific Reports

Phylogenetic relatedness, phenotypic similarity and plant–soil feedbacks – Connor R. Fitzpatrick

Review: Microbiome and the future for food and nutrient security – Brajesh K. Singh – Microbial Biotechnology

Water microbiome

Similar community assembly mechanisms underlie similar biogeography of rare and abundant bacteria in lakes on Yungui Plateau, China – Jingqiu Liao – Limnology and Oceanography

Built environment microbiome

Microbial diversity in different compartments of an aquaponics system – Zala Schmautz – Archives of Microbiology

Food microbiology

The influence of thiamine and riboflavin on various spoilage microorganisms commonly found in beer – Barry Hucker – The Journal of The Institue of Brewing

Waste and pollution microbiology

Microbial flora analysis for the degradation of beta-cypermethrin – Zhang Qi – Environmental Science and Pollution Research

Fungi (also see Animal Microbiome)

Medical mycology and fungal immunology: new research perspectives addressing a major world health challenge – Neil A. R. Gow – Philosophical Transactions of the Royal Society B

Proteomics and metabolomics

MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota – Aitor Blanco-Míguez – Database

PerspectiveProgress in the biology and analysis of short chain fatty acids – Roel J. Vonk – The Journal of Physiology

Bioinformatics and biostatistics

Using Machine Learning to Identify Major Shifts in Human Gut Microbiome Protein Family Abundance in Disease – Mehrdad Yazdani – IEEE

Microscale Insight into Microbial Seed Banks – Kenneth J. Locey – Frontiers in Microbiology

* EMPeror: Bringing the Dynamic Microbiome to Life with Animations – Yoshiki Vázquez-Baeza – Cell Host & Microbe

Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities – Gongchao Jing – Scientific Reports

Identifying Host Genetic Variants Associated with Microbiome Composition by Testing Multiple Beta Diversity Matrices – Hua X. – Human Heredity

MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets – Xilin Xu – Biophysics Reports

Techniques

Methodological flaws introduce strong bias into molecular analysis of microbial populations – N. Krakat – Journal of Applied Microbiology

Editorial: Microbial Nanoscopy: Breakthroughs, Challenges, and Opportunities – Yves F. Dufrêne – ACS Nano

More microbes

Asgard archaea illuminate the origin of eukaryotic cellular complexity – Katarzyna Zaremba-Niedzwiedzka – Nature

* Species-Independent Attraction to Biofilms through Electrical Signaling – Jacqueline Humphries – Cell

A bacterial global regulator forms a prion – Andy H. Yuan – Science

A periplasmic polymer curves Vibrio cholerae and promotes pathogenesis – Thomas M. Bartlett – Cell

Assembly of a nucleus-like structure during viral replication in bacteria – Vorrapon Chaikeeratisak – Science

Microbes in the news

Man’s best friend, bacteria’s worst enemy: dog sniffs out superbug in Canadian hospital – Ashifa Kassam – The Guardian

This article is not as bad as the title suggests but with photoshopped images:
Revealed: The millions of stomach-churning bacteria lurking in YOUR hair, skin, lungs, gut and mouth – and why – Mary Kekatos – Daily Mail

Video: Career profiles: Program Director at National Science Foundation Matthew Kane – American Society for Microbiology

A clear picture of bacteria: A new study has frozen bacteria extremely fast to gain a true-to-nature image of the internal and external structure – Science Daily