March 17, 2018

A packed microbiome digest today, particularly if you want to indulge in a gut microbiome review or some soil microbiome discoveries. There is also a nice microbial perspective on the life‐history evolution of marine invertebrate larvae!



Report of the San Francisco Bay Area Microbiome Meetup group


Scientific Officer (Microbiology) – Hyper Recruitment Solutions – Wiltshire, UK

Assistant professor in Reproductive Health Sciences with focus on the microbiome – Karolinska Institutet – Sweden

Human respiratory microbiome

Chronic Rhinosinusitis: Potential Role of Microbial Dysbiosis and Recommendations for Sampling Sites – Elizabeth Copeland – Frontiers in Cellular and Infection Microbiology

Human gut microbiome

 Can microbiology affect psychiatry? A link between gut microbiota and psychiatric disorders – Ewelina Gulas  – Psychiatria Polska

A Lachnospiraceae-dominated bacterial signature in the fecal microbiota of HIV-infected individuals from Colombia, South America – Homero San-Juan-Vergara – Scientific Reports

Preprint: Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids – Sara C. Di Rienzi – BioRxiv

A systematic review of studies on the faecal microbiota in anorexia nervosa: future research may need to include microbiota from the small intestine – Hanna Ferløv Schwensen – Eating and Weight Disorders – Studies on Anorexia, Bulimia and Obesity

Systematic Review: Gut Microbiota in Fecal Samples and Detection of Colorectal Neoplasms – Efrat L. Amitay – Gut Microbes

How are the expression patterns of gut antimicrobial peptides modulated by human gastrointestinal diseases? A bridge between infectious, inflammatory, and malignant diseases – Paulo André Dias Bastos – Journal of the European Peptide Society EPS

Animal experiments

Prebiotic attenuation of olanzapine-induced weight gain in rats: analysis of central and peripheral biomarkers and gut microbiota – Amy Chia-Ching Kao – Translational Psychiatry

Adverse effect of early-life high-fat/high-carbohydrate (“Western”) diet on bacterial community in the distal bowel of mice – Sandra InfanteVillamil – Nutrition Research

Animal microbiome

A microbial perspective on the life‐history evolution of marine invertebrate larvae: If, where and when to feed – Tyler J. Carrier – Marine Ecology

The significance of the diversity and composition of the cecal microbiota of the Tibetan swine – Weiping Yang – Annals of Microbiology

A global comparison of the microbiome compositions of three gut locations in commercial pigs with extreme feed conversion ratios – Jianping Quan – Scientific Reports

Holobionts and ecological speciation: the intestinal microbiota of lake whitefish species pairs – Maelle Sevellec – Microbiome

Plant, root, and soil microbiome

 Are the microbial communities involved in glucose assimilation in paddy soils treated with different fertilization regimes for three years similar? – Yali Kong – Journal of Soils and Sediments

Comparison of crop productivity and soil microbial activity among different fertilization patterns in red upland and paddy soils – Liu Kai-lou – Acta Ecologica Sinica

Application of manure containing tetracyclines slowed down the dissipation of tet resistance genes and caused changes in the composition of soil bacteria – WenguangXiong – Ecotoxicology and Environmental Safety

Soil pH is equally important as salinity in shaping bacterial communities in saline soils under halophytic vegetation – Shuai Zhao – Scientific Reports

Glyphosate application increased catabolic activity of gram-negative bacteria but impaired soil fungal community – Yehao Liu – Environmental Science and Pollution Research

Bacterial community structure and diversity responses to the direct revegetation of an artisanal zinc smelting slag after 5 years – Youfa Luo – Environmental Science and Pollution Research

 Water and extremophile microbiome

Incubation with macroalgae induces large shifts in water column microbiota, but minor changes to the epibiota of cooccurring macroalgae – Melissa Y Chen – Molecular Ecology


Review and perspective on mathematical modeling of microbial ecosystems – Antonella Succurro – Biochemical Society Transactions


DNA extraction for streamlined metagenomics of diverse environmental samples – Clarisse Marotz – BIOTECHNIQUES

Microbes in the news

Sensitive Microbial Test Identifies Previously Undetectable Bacteria –  Genetic Engineering & Biotechnology News



December 28, 2017

Not many microbiome articles today, but a good selection non the less! Dysbiosis and obesity in humans, effects of hay on suckling calfs, and MPLasso to Infer microbial association networks.

Human respiratory microbiome

The impact of persistent bacterial bronchitis on the pulmonary microbiome of children – Leah Cuthbertson – PLOS ONE

Human vaginal microbiome

The vaginal microbiome and sexually transmitted infections are interlinked: Consequences for treatment and prevention – Janneke H. H. M. van de Wijgert – PLOS Medicine

Human gut microbiome

Dysbiosis Signatures of Gut Microbiota Along the Sequence from Healthy, Young Patients to Those with Overweight and Obesity – Renyuan Gao – Obesity

The NLR Protein NLRP6 Does Not Impact Gut Microbiota Composition – Paul Lemire – Cell Reports


Animal experiments

Effect of hay supplementation timing on rumen microbiota in suckling calves – Xueyan Lin – MicrobiologyOpen

Shaping of Intestinal Microbiota in Nlrp6- and Rag2-Deficient Mice Depends on Community Structure – Eric J.C. Gálvez – Cell Reports

Animal microbiome

Associations between Escherichia coli O157 shedding and the fecal microbiota of dairy cows – Chloe Stenkamp-Strahm – Journal of Applied Microbiology

Taxonomic differences of gut microbiomes drive cellulolytic enzymatic potential within hind-gut fermenting mammals – Emma C. L. Finlayson-Trick – PLOS ONE

Plant, root, and soil microbiome

Shift of allelochemicals from Sorghum halepense in the soil and their effects on the soil’s bacterial community – Hongjuan Huang – Weed Biology and Management



MPLasso: Inferring microbial association networks using prior microbial knowledge – Chieh Lo – PLOS Computational Biology

December 27, 2017

Quite a few papers on the gut microbiome today, in addition to coral reef microbiomes and the sinonasal microbiome.


Human respiratory microbiome

The sinonasal microbiota, neural signaling, and depression in chronic rhinosinusitis – Michael Hoggard – International Forum of Allergy & Rhinology

Human skin microbiome

Clostridia in the gut and onset of atopic dermatitis via eosinophilic inflammation – Eun Lee – Annals of Allergy, Asthma & Immunology 

Human gut microbiome

In vitro human colonic fermentation of indigestible fraction isolated from lunch menus: impact on the gut metabolites and antioxidant capacity – Victor Manuel Zamora-Gasga – International Journal of Food Sciences and Nutrition

Targeting gut microbiome: A novel and potential therapy for autism – Yongshou Yang – Life Sciences

Molecular mechanistic pathway of colo-rectal carcinogenesis associated with intestinal microbiota – Paramita Mandal – Anaerobe

Gut microbiota and obesity: implications for fecal microbiota transplantation therapy – Yongbo Kang – HORMONES

Correlation between gut microbiota and personality in adults: a cross-sectional study – Han-Na Kim – Brain, Behavior, and Immunity

Randomized clinical trial to evaluate the effect of fecal microbiota transplant for initial Clostridium difficile infection in intestinal microbiome – Adrián Camacho-Ortiz – PLOSone

Water and extremophile microbiome

Interplay between stochastic and deterministic processes in the maintenance of alternative community states in Verrucomicrobia-dominated shallow lakes – Maria E. Llames – FEMS Microbiology Ecology

Complex interactions between potentially pathogenic, opportunistic, and resident bacteria emerge during infection on a reef-building coral – Sarah A. Gignoux-Wolfsohn – FEMS Microbiology Ecology

Bacterial community composition and diversity in Kalakuli, an alpine glacial-fed lake in Muztagh Ata of the westernmost Tibetan Plateau – Keshao Liu – FEMS Microbiology Ecology

December 10, 2017

Microbiology jobs and a PhD are posted today along with a review of microbiota and aging, and research looking at if/how the Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients. Plus a slew of other research highlights –  Enjoy!


Events and jobs

PhD: Mining and Modelling the Human Gut Microbiome to Elucidate its Metabolic Potential – Aberdeen University

Professor or Associate Professor – Medical Microbiology – University of Oslo

Part-Time Microbiology Laboratory Technician – Miami Dade College

Microbiology Laboratory Manager – Georgia Department of Public Health

General microbiome

Review: Microbiota and Aging. A Review and Commentary – Carmen García-Peña – Archives of Medical Research

 Pregnancy and early life

Influence of the intestinal microbiota on the immunogenicity of oral rotavirus vaccine given to infants in south India – Edward P.K. Parker – Vaccine

 Human respiratory microbiome

Microbial diversity within the airway microbiome in chronic pediatric lung diseases – Andrea Hahn – Infection, Genetics and Evolution

Compositional and functional variations of oral microbiota associated with the mutational changes in oral cancer – Shun-Fa Yang – Oral Oncology

 Human gut microbiome

Metabolic analysis of Panax notoginseng saponins with gut microbiota-mediated biotransformation by HPLC-DAD-Q-TOF-MS/MS – Man-Yun Chen – Journal of Pharmaceutical and Biomedical Analysis

Towards utilization of the human genome and microbiome for personalized nutrition – Stavros Bashiardes – Current Opinion in Biotechnology

Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients – V. Gopalakrishnan – Science

 Animal microbiome

Co-occurrence of early gut colonization in neonatal piglets with microbiota in the maternal and surrounding delivery environments – Xue Chen – Anaerobe

 Plant, root, and soil microbiome

Ralstonia solanacearum pathogen disrupts bacterial rhizosphere microbiome during an invasion – Zhong Wei – Soil Biology and Biochemistry

Substrate-driven microbial response: A novel mechanism contributes significantly to temperature sensitivity of N2O emissions in upland arable soil – Alin Song – Soil Biology and Biochemistry

 Water and extremophile microbiome

Environmental DNA metabarcoding of benthic bacterial communities indicates the benthic footprint of salmon aquaculture – Thorsten Stoeck – Marine Pollution Bulletin

 Probiotics / prebiotics

The Role of Prebiotics and Probiotics in Gastrointestinal Disease – Martin H. Floch – Gastroenterology Clinics of North America

Alzheimer’s disease and gut microbiota modifications: the long way between preclinical studies and clinical evidence – Cesare Mancuso – Pharmacological Research

Microbes in the news

It might be possible to remodel a baby’s microbiome (But we still don’t really know what a healthy microbiome really is) – PopularScience


December 9, 2017

Do you want to know what microbes are in the international space station? the effects of Arsenic exposure on childrens microbiomes? or perhaps you are interested in tree leaf bacterial diversity along an urban gradient?  Well, today we have it all and more! Enjoy Saturdays microbiome digest for links to the latest research on microbiomes.


General microbiome

Microbial Ecology: Community Coalescence Stirs Things Up – Matthias C. Rillig – Current Biology

Multi-site human microbiome

Distinct fecal and oral microbiota composition in human type 1 diabetes, an observational study – Pieter F. de Groot – PlosONE

Human skin microbiome

The role of the skin microbiome in atopic dermatitis: a systematic review – R.D. Bjerre – British Journal of Dermatology

Human gut microbiome

Preprint: Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Patients with Celiac Disease and Controls – Sudarshan A Shetty et al – BioRxiv

Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function – Noel T. Mueller et al – Genes

Correlations between gut microbiota community structures of Tibetans and geography – Daoliang Lan et al – Scientific Reports

Arsenic exposure and intestinal microbiota in children from Sirajdikhan, Bangladesh – Xiaoxi Dong – PlosONE

The role of gut microbiota in the modulation of drug action: A focus on some clinically significant issues – Diego Currò – Expert Review of Clinical Pharmacology

Review: Codevelopment of Microbiota and Innate Immunity and the Risk for Group B Streptococcal Disease – Julia Kolter – Frontiers in Immunology

Animal experiments

Glucerabacter canisensis gen. nov., sp. nov., isolated from dog feces and its effect on the hydrolysis of plant glucosylceramide in the intestine of dogs – Misho Kawata et al – Archives of Microbiology

Meta-Analysis of Fecal Microbiota and Metabolites in Experimental Colitic Mice during the Inflammatory and Healing Phases – Toshifumi Osaka – Nutrients

Animal microbiome

Hierarchical social networks shape gut microbial composition in wild Verreaux’s sifaka – Amanda C. Perofsky – Proceedings of the Royal Society B

Plant, root, and soil microbiome

Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity – Isabelle Laforest-Lapointe – mSystems

Microbial and Plant-Assisted Bioremediation of Heavy Metal Polluted Environments: A Review – Omena Bernard Ojuederie and Olubukola Oluranti Babalola – International Journal of Environmental Research and Public Health

Soil microbial communities of three grassland ecosystems in the Bayinbuluke, China – Keqiang Shao – Canadian Journal of Microbiology

Response of soil microbial community dynamics to Robinia pseudoacacia L. afforestation in the loess plateau: a chronosequence approach – Jinliang Liu – Plant and Soil

Microbes in space

A microbial survey of the International Space Station – Jenna M. Lang et al – PeerJ

November 22, 2017

Todays roundup of microbiome research highlights studies of wound microbiomes, the Influences of quorum-quenching probiotic bacteria (in pigs), and plant–fungal nutrient trading, to name but a few! Enjoy!


General microbiome

Gut Feeling: Researchers Are Discovering a Link Between Depression and Gut Bacteria – Mary Bates, IEEE Pulse

Human respiratory microbiome

Bacterial microbiota of the nasal passages across the span of human life – Lindsey Bomar et al, Current Opinion in Microbiology

Human skin microbiome

Development, standardization and testing of a bacterial wound infection model based on ex vivo human skin – Christoph Schaudinn et al, PLOS ONE

Measuring the microbiome of chronic wounds with use of a topical antimicrobial dressing – A feasibility study – Lindsay Kalan et al, PLOS ONE

A dysbiotic mycobiome dominated by Candida albicans is identified within oral squamous-cell carcinomas – Manosha Perera et al, Journal of Oral Microbiology

Animal experiments

Influences of quorum-quenching probiotic bacteria on the gut microbial community and immune function in weaning pigs – Jonggun Kim et al, Animal Science Journal

Faecal microbiota in dogs with multicentric lymphoma – A. Gavazza et al, Veterinary and Comparative Oncology

Animal microbiome

Intestinal microbiota profiles associated with low and high residual feed intake in chickens across two geographical locations – Sina-Catherine Siegerstetter et al, PLOS ONE

Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species – Per Eriksson et al, Infection Ecology & Epidemiology

Plant, root, and soil microbiome

Root type and soil phosphate determine the taxonomic landscape of colonizing fungi and the transcriptome of field-grown maize roots – Peng Yu et al, New Phytologist

Role of plant–fungal nutrient trading and host control in determining the competitive success of ectomycorrhizal fungi – Sara Hortal et al, The ISME Journal

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level – Yuji Jiang et al, The ISME Journal

Habitat- and soil-related drivers of the root-associated fungal community of Quercus suber in the Northern Moroccan forest – Fatima Zahra Maghnia et al, PLOS ONE

Water and extremophile microbiome

Changes in nutrient stoichiometry, elemental homeostasis and growth rate of aquatic litter-associated fungi in response to inorganic nutrient supply – Vladislav Gulis et al, The ISME Journal

Host-genotype dependent gut microbiota drives zooplankton tolerance to toxic cyanobacteria – Emilie Macke et al, Nature Communications

Probiotics / prebiotics

Simulating colonic survival of probiotics in single-strain products compared to multi-strain products – S. D. Forssten et al, Microbial Ecology in Health and Disease


dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication – Matthew R Olm, The ISME Journal

July 30, 2017

Relax into your Sunday and read through the days new microbiome research


Events and jobs

Laboratory Technician-Microbiology – Wilmington, DE

Pregnancy and early life

Maternal modifiers of the infant gut microbiota: metabolic consequences – Christopher M Mulligan – Journal of Endocrinology

Human respiratory microbiome

Composition and abundance of microbiota in the pharynx in patients with laryngeal carcinoma and vocal cord polyps – Hongli Gong – Journal of Microbiology

Human gut microbiome

Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis – Chengping Wen – Genome Biology

Persistent diarrhea: A persistent infection with enteropathogens or a gut commensal dysbiosis? – Shafiqul A. Sarker – Environmental Microbiology

Reproducibility of assessing fecal microbiota in chronic constipation – G. Parthasarathy – Neurogastroenterology & Motility

Effects of mushroom consumption on the microbiota of different target groups – Impact of polyphenolic composition and mitigation on the microbiome fingerprint – Emanuel Vamanu – LWT – Food Science and Technology

Shotgun metagenomic data on the human stool samples to characterize shifts of the gut microbial profile after the Helicobacter pylori eradication therapy – Eugenia A. Boulygina – Data in Brief

Review: Strategies to increase the efficacy of using gut microbiota for the modulation of obesity – J. Li – Obesity Reviews

Animal experiments 

Amino acid metabolic signaling influences Aedes aegypti midgut microbiome variability – Sarah M. Short – PLOS One

Differential intestinal anti-inflammatory effects of Lactobacillus fermentum and Lactobacillus salivarius in DSS mouse colitis: impact on microRNAs expression and microbiota composition – Alba Rodríguez-Nogales – Molecular Nutrition & Food Research

Animal microbiome

Links between Natural Variation in the Microbiome and Host Fitness in Wild Mammals – Taichi A. Suzuki – Integrative and Comparative Biology

Captivity Shapes the Gut Microbiota of Andean Bears: Insights into Health Surveillance – Andrea Borbón-García – Frontiers in Microbiology

Microbiomes of American Oysters (Crassostrea virginica) Harvested from Two Sites in the Chesapeake Bay – Sylvia Ossai – Genome Announcements

Rumen Microbiome, Probiotics, and Fermentation Additives – Joshua C. McCann – Veterinary Clinics of North America: Food Animal Practice

Plant, root, and soil microbiome

Assessing the influence of farm fertility amendments, field management, and sorghum genotypes on soil microbial communities and grain quality – Adam B. Cobb – Applied Soil Ecology

Rhizospheric Microbiome Profiling of Capsicum annuum L. Cultivated in Amended Soils by 16S and Internal Transcribed Spacer 2 rRNA Amplicon Metagenome Sequencing – Ali Asaff-Torres – Genome Announcements

Peaks of in situ N2O emissions are influenced by N2O producing and reducing microbial communities across arable soils – L.A Domeignoz-Horta – Global Change Biology

Eelgrass Leaf Surface Microbiomes Are Locally Variable and Highly Correlated with Epibiotic Eukaryotes – Mia M. Bengtsson – Frontiers in Microbiology

Microbial community structure is affected by cropping sequences and poultry litter under long-term no-tillage – A.J. Ashworth – Soil Biology and Biochemistry

Interaction of microorganisms within leafy green phyllospheres: Where do human noroviruses fit in? – Wenjun Deng – International Journal of Food Microbiology

Water and extremophile microbiome

Spatial and Temporal Microbial Patterns in a Tropical Macrotidal Estuary Subject to Urbanization – Mirjam Kaestli – Frontiers in Microbiology

Evidence of microbial rhodopsins in Antarctic Dry Valley edaphic systems – Leandro D. Guerrero – Environmental Microbiology

Prokaryotic diversity and community composition in the Salar de Uyuni, a large scale, chaotropic salt flat – Sergio S. Rubin – Environmental Microbiology

Fate of antibiotic resistance genes and their associations with bacterial community in livestock breeding wastewater and its receiving river water – Shuyu Jia – Water Research

Performance and microbial community analysis of a microaerophilic sulfate and nitrate co-reduction system – Xi-Jun Xu – Chemical Engineering Journal

Characteristics of microbial community functional structure of a biological coking wastewater treatment system – Dev Raj Joshi – Journal of Environmental Sciences

Food microbiology

Evolution of microbial community and chemical properties of a sourdough during the production of Colomba, an Italian sweet leavened baked product – Stefano Raimondi – LWT – Food Science and Technology

Bacterial community diversity of traditional fermented vegetables in China – Daqun Liu – LWT – Food Science and Technology