November 18, 2018

Do your eyes have microbiomes? How does heavy rain influence the Atacama desert microbiome?  Welcome to the microbiome digest. This weekends articles also include the latest research on space-station microbes, the influence of protists on the rhizosphere, techniques in metabolome/microbiome research and more! Enjoy!

General microbiome

Identifying and Predicting Novelty in Microbiome Studies – Xiaoquan Su – mBio

Pregnancy and early life

Impacts of diet and exercise on maternal gut microbiota are transferred to offspring – Shyam Prakaash Bhagavata Srinivasan – Frontiers in Endocrinology

Multi-site human microbiome

Biogeography of the human ocular microbiota – JeromeOzkan – The Ocular Surface

Review: The Human Microbiota and Asthma – Aaron Ver Heul – Clinical Reviews in Allergy & Immunology

Human gut microbiome

Gastroduodenal “Dysbiosis”: a New Clinical Entity – Ayesha Shah – Current Treatment Options in Gastroenterology

Animal experiments

Preprint: Colonization of the tsetse fly midgut with commensal Enterobacter inhibits trypanosome infection establishment – Brian L Weiss – bioRiv

Animal microbiome

Association of bovine major histocompatibility complex (BoLA) gene polymorphism with colostrum and milk microbiota of dairy cows during the first week of lactation – Hooman Derakhshani – Microbiome

Plant, root, and soil microbiome

Protists: Puppet Masters of the Rhizosphere Microbiome – ZhileiGao – Trends in Plant Science

Characterization of microbes and denitrifiers attached to two species of floating plants in the wetlands of Lake Taihu – Bing Han – PLOS ONE

Environmental and spatial variables determine the taxonomic but not functional structure patterns of microbial communities in alpine grasslands – Xiao-BoWang – Science of The Total Environment

With or without trees: Resistance and resilience of soil microbial communities to drought and heat stress in a Mediterranean agroforestry system – EstherGuillot – Soil Biology and Biochemistry

Response of microbial communities and enzyme activities to amendments in saline-alkaline soils – ShaohuaShi – Applied Soil Ecology

The effect of moisture on soil microbial properties and nitrogen cyclers in Mediterranean sweet orange orchards under organic and inorganic fertilization – AliciaMorugán-Coronado – Science of The Total Environment

Water and extremophile microbiome

Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces – Nitin Kumar Singh – Microbiome

Unprecedented rains decimate surface microbial communities in the hyperarid core of the Atacama Desert – A. Azua-Bustos – Scientific Reports

Exposure to tetracycline perturbs the microbiome of soil oligochaete Enchytraeus crypticus – JunMa – Science of The Total Environment

Preprint: Filamentation of Vibrio cholerae is an adaptation for surface attachment and biofilm architecture – Benjamin R Wucher – bioRxiv

Designing an in situ remediation strategy for polluted surface water bodies through the specific regulation of microbial community – Boran Wu – Frontiers of Environmental Science & Engineering

Food microbiology

Microbiome of drinking water: A full-scale spatio-temporal study to monitor water quality in the Paris distribution system – YoannPerrin – Water Research


Mass Spectrometry-Based Microbial Metabolomics: Techniques, Analysis, and Applications – Edward E. K. Baidoo – Microbial Metabolomics

High-Throughput Solid-Phase Microextraction–Liquid Chromatography–Mass Spectrometry for Microbial Untargeted Metabolomics – Fatemeh Mousavi – Microbial Metabolomics

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