June 5, 2019

Today’s short Digest features many preprints, including an attempt to explain the emergence of a multi-drug resistant fungal pathogen, and another piece of evidence for the placenta microbiome?

Antimicrobial resistance

A novel anti Candida albicans drug screening system based on high-throughput microfluidic chips – Le Qiang et al. – Scientific Reports

** Preprint: On the emergence of Candida auris: climate change, azoles, swamps and birds – Arturo Casadevall et al. – bioRxiv

Preprint: The Evolution of Fluoroquinolone-Resistance in Mycobacterium tuberculosis is Modulated by the Genetic Background – Rhastin A. D. Castro et al. – bioRxiv

Pregnancy and early life

** Preprint: Placenta microbiome diversity is associated with maternal pre-pregnancy obesity and placenta biogeography – Paula Benny et al. – bioRxiv

Human gut microbiome

Preprint: Pneumococcal Colonisation is an Asymptomatic Event in Healthy Adults using an Experimental Human Colonisation Model – Ashleigh Trimble et al. – bioRxiv

Plant, root and soil microbiome

The effects of chemical and organic fertilizer usage on rhizosphere soil in tea orchards – Weiwei Lin et al. – PLoS One

Preprint: Root development is maintained by specific bacteria-bacteria interactions within a complex microbiome – Omri M. Finkel et al. – bioRxiv

Water and extremophile microbiome

Preprint: Hyperdiverse archaea near life limits at the polyextreme geothermal Dallol area – Jodie Belilla et al. – bioRxiv

Phages and viruses

Recombinant Strains of Human Parechovirus in Rural Areas in the North of Brazil – Élcio Leal et al. – Viruses

Preprint: Dynamic pneumococcal genetic adaptations support bacterial growth and inflammation during coinfection with influenza – Amanda P Smith et al. – bioRxiv


May 24, 2019

Today we have a short Digest before the Memorial Day weekend in America. Highlights include a comparative metabolomic study on Mycobacterium tuberculosis and a live attenuated strain as a potential vaccine, a report on oral cavity resistome worldwide and last but not least, fossils of early fungi that are about 1 billion years old!

General microbiology

Quorum Sensing Circuits in the Communicating Mechanisms of Bacteria and Its Implication in the Biosynthesis of Bacteriocins by Lactic Acid Bacteria: a Review – Ourdia Kareb & Mohammed Aïder – Probiotics and Antimicrobial Proteins

** Early fungi from the Proterozoic era in Arctic Canada – Corentin C. Loron et al. – Nature

Antimicrobial resistance

** Preprint: Abundance and diversity of resistomes differ between healthy human oral cavities and gut – Victoria R. Carr et al. – bioRxiv

Human skin microbiome

Skin Microbiome Differences in Atopic Dermatitis and Healthy Controls in Egyptian Children and Adults, and Association with Serum Immunoglobulin E – Mohammed Ramadan et al. – OMICS: A Journal of Integrative Biology

Review: Microbiome and skin biology – Lunjani, Nonhlanhla et al. – Current opinion in allergy and clinical immunology

Human oral microbiome

Intra‐oral single site comparisons of periodontal and peri‐implant microbiota in health and disease – Xiao‐Lin Yu et al. – Clinical Oral Implants Research

Built environment microbiome

Spatial Gradients of Fungal Abundance and Ecology throughout a Damp Building – Bridget Hegarty et al. – Environmental Science & Technology Letters


** COMPARATIVE METABOLOMICS BETWEEN Mycobacterium tuberculosis AND THE MTBVAC VACCINE CANDIDATE – Caridad Díaz Navarro et al. – ACS Infectious Diseases

Animal microbiome

The Role of Tissue Type, Sampling and Nucleic Acid Purification Methodology on the Inferred Composition of Pacific Oyster (Crassostrea gigas) Microbiome – Erandi Pathirana et al. – Journal of Applied Microbiology

Plant, root and soil microbiome

Vertical distribution of microbial communities in chromium-contaminated soil and isolation of Cr(Ⅵ)-Reducing strains – Bang Liu & Guirong Su et al. – Ecotoxicology and Environmental Safety

Preprint: Root development is maintained by specific bacteria-bacteria interactions within a complex microbiome – Omri M. Finkel et al. – bioRxiv

Microbes in the news

Microbiome: Small Organisms Play Big Shots in Plants – Soumya Kumar Sahoo et al. – Biomolecule Reports

May 3, 2019

A concise Digest today featuring a novel approach to targeting antibiotic resistance, and some cool art by a Healthcare company to promote infectious disease awareness. Enjoy reading! (Apologies for the tight formatting, technological difficulty…)
General microbiology
Review: Fungal evolution: major ecological adaptations and evolutionary transitions – Miguel A. Naranjo-Ortiz and Toni Gabaldón – Biological Reviews
Antibiotic resistance
Pregnancy and early life
Household composition and the infant fecal microbiome: The INSPIRE study – Avery A. Lane et al. – American Journal of Physical Anthropology
Human skin microbiome
Human reproductive microbiome
Cancer microbiome
Review: Culture-independent studies on bacterial dysbiosis in oral and oropharyngeal squamous cell carcinoma: A systematic review – Divya Gopinatha & Rohit Kunnath Menonb et al. – Critical reviews Oncology Hematology
Animal experiments
Plant, root and soil microbiome
Microbes in the news
‘Microbiome’ May Be Key to Autism Symptoms – Serena Gordon – Health Day


April 24, 2019

Today’s rich Digest features a report on how an invasive fungus restructures bat skin microbiome and a review on how plant-based culture media might come about. How is authorship determined? Enjoy reading!

Human gut microbiome

Review: Gut Microbiota in Alzheimer’s Disease, Depression, and Type 2 Diabetes Mellitus: The Role of Oxidative Stress – Maria Luca et al. – Oxidative Medicine and Cellular Longevity

Cancer microbiome

Review: Exploring the emerging role of the microbiome in cancer immunotherapy – Jessica Fessler & Vyara Matson et al. – Journal for ImmunoTherapy of Cancer

Salivary Microbial Dysbiosis is Associated with Systemic Inflammatory Markers and Predicted Oral Metabolites in Non-Small Cell Lung Cancer Patients – Weiquan Zhang et al. – Journal of Cancer


Review: Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community – Farhana R. Pinu et al. – Metabolites

BLANKA: an Algorithm for Blank Subtraction in Mass Spectrometry of Complex Biological Samples – Jessica L. Cleary et al. – Journal of The American Society for Mass Spectrometry

Review: Comparative genomics and metagenomics of the metallomes – Yan Zhang et al. – Metallomics

Animal experiments

Analysis of the In Vivo Transcriptome of Bordetella pertussis during Infection of Mice – Ting Y. Wong et al. – mSphere

Structural modulation of gut microbiota reveals Coix seed contributes to weight loss in mice – Sheng Liu et al. – Applied Microbiology and Biotechnology

Supplementation with compound polysaccharides contributes to the development and metabolic activity of young rat intestinal microbiota – Mengxia Wang et al. – Food & Function

Animal microbiome

Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua) – Typhaine Le Doujet et al. – Microbiome

Comparative analysis of intestinal bacteria among venom secretion and non-secrection snakes – Zuodong Qin et al. – Scientific Reports

Parallel sequencing of porA reveals a complex pattern of Campylobacter genotypes that differs between broiler and broiler breeder chickens – Frances. M. Colles et al. – Scientific Reports

** Preprint: White-nose syndrome restructures bat skin microbiomes – Meghan A. Ange-Stark et al. – bioRxiv

Food microbiome

Establishment limitation constrains the abundance of lactic acid bacteria in the Napa cabbage phyllosphere – Esther R. Miller et al. – Applied and Environmental Microbiology

Plant, root and soil microbiome

Unprecedented bacterial community richness in soybean nodules vary with cultivar and water status – Hazem Sharaf et al. – Microbiome

Fungi Originating From Tree Leaves Contribute to Fungal Diversity of Litter in Streams – Pirjo Koivusaari et al. – Frontiers in Microbiology

Successional trajectories of soil bacterial communities in mine tailings: The role of plant functional traits – Yannick Colin et al. – Journal of Environmental Management

Elevated CO2, chlorpyrifos and biochar influence nitrification and microbial abundance in the rhizosphere of wheat cultivated in a tropical vertisol – Bharati Kollah et al. – Rhizosphere

Increasing livestock wastewater application in alternate-furrow irrigation reduces nitrification gene abundance but not nitrification rate in rhizosphere – Yuan Liu et al. – Biology and Fertility of Soils

** Review: Culturomics of the plant prokaryotic microbiome and the dawn of plant-based culture media – A review – Mohamed S. Sarhan et al. – Journal of Advanced Research

Water and extremophile microbiome

Coupling growth kinetics modeling with machine learning reveals microbial immigration impacts and identifies key environmental parameters in a biological wastewater treatment process – Ran Mei et al. – Microbiome

Fungal Community Composition and Potential Depth-Related Driving Factors Impacting Distribution Pattern and Trophic Modes from Epi- to Abyssopelagic Zones of the Western Pacific Ocean – Wei Li et al. – Microbial Ecology

Different response of bacteria, archaea and fungi to process parameters in nine full-scale anaerobic digesters – Susanne G. Langer et al. – Microbial Biotechnology

Increasing livestock wastewater application in alternate-furrow irrigation reduces nitrification gene abundance but not nitrification rate in rhizosphere – Yuan Liu et al. – Biology and Fertility of Soils

Oil Hydrocarbon Degradation by Caspian Sea Microbial Communities – John I. Miller et al. – Frontiers in Microbiology

Bacterial Community 16S rRNA Gene Sequencing Characterizes Riverine Microbial Impact on Lake Michigan – Cindy H. Nakatsu et al. – Frontiers in Microbiology

Patterns of bacterial and archaeal communities in sediments in response to dam construction and sewage discharge in Lhasa River – Ke Tao et al. – Ecotoxicology and Environmental Safety

Potentially toxic metal contamination and microbial community analysis in an abandoned Pb and Zn mining waste deposit – M.C. Kasemodel et al. – Science of The Total Environment

Structure and function of microbial community associated with phenol co-substrate in degradation of benzo[a]pyrene in coking wastewater – Haizhen Wu et al. – Chemosphere

Phages and viruses

Distribution and Phylogeny of Erythrocytic Necrosis Virus (ENV) in Salmon Suggests Marine Origin – Veronica A. Pagowski et al. – Viruses

Interaction of RNA viruses of the natural virome with the African malaria vector, Anopheles coluzzii – Ferdinand Nanfack-Minkeu et al. – Scientific Reports


Active harvesting enhances energy recovery and function of electroactive microbiomes in microbial fuel cells – Lu Lu et al. – Applied Energy


Letter to Editor: Towards precision quantification of contamination in metagenomic sequencing experiments – M. S. Zinter et al. – Microbiome

Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data – Krithika Arumugam et al. – Microbiome

Review: Evolution of biosequence search algorithms: a brief survey – Gregory Kucherov – Bioinformatics

Microbes in the news

Two new studies reveal universal gut microbiome signatures in colorectal cancer – Andreu Prados – Gut Microbiota for Health

Prime the Pump – Robert B Corbett – Bovine Vet Online

Germ-Killing Brands Now Want to Sell You Germs – Caroline Winter – Bloomberg

Podcast: What is Functional Medicine’s Role In Gut Healing? – The Microbiome Report

Microbes on the market

Viome Raised $25M for its Microbiome-based Dietary Guide Platform – Chris Albrecht – The Spoon

Non-microbiology pick

** Preprint: A qualitative study exploring researchers’ perspectives on authorship decision-making – Lauren A Maggio et al. – bioRxiv

April 17, 2019

Today’s Digest contains quite a few news articles. Features for today include a review on the importance of proper controls in microbiome studies, a patent for one method of analyzing microbiome dynamics (really?), and the NASA Twins Study, how can one year in space change your gut microbiota and much more? Enjoy reading!

General microbiology

Guideline: Microbiology Investigation Criteria for Reporting Objectively (MICRO): a framework for the reporting and interpretation of clinical microbiology data – Paul Turner & Andrew Fox-Lewis et al. – BMC Medicine

** Patent: Method of analyzing microbiome – E Segal & E Elinav

Combined deterministic and stochastic processes control microbial succession in replicate granular biofilm reactors – R Liébana et al. – Environmental Science & Technology

** Uncorrected proof: Issues and current standards of controls in microbiome research – Bastian V.H. Hornung et al. – FEMS Microbiology Ecology

Pregnancy and early life

Review: Intestinal Microbiota in Early Life and Its Implications on Childhood Health – Lu Zhuang et al. – Genomics, Proteomics & Bioinformatics

Cancer microbiome

PDF: Gastric Microbiota in Helicobacter pylori-Negative and -Positive Gastritis Among High Incidence of Gastric Cancer Area – Boldbaatar Gantuya et al. – Cancers

Human respiratory microbiome

Review: Microbes, metabolites, and the gut–lung axis – Anh Thu Dang & Benjamin J. Marsland – Mucosal Immunology

Microbial contributions to bronchial asthma occurrence in children: A metagenomic study – Man Tian et al. – Journal of Cellular Biochemistry

Human gut microbiome

Review: A Review on Bile Acids: Effects of the Gut Microbiome, Interactions with Dietary Fiber, and Alterations in the Bioaccessibility of Bioactive Compounds – Jashbir Singh et al. – Journal of Agricultural and Food Chemistry

Increased mucosal neutrophil survival is associated with altered microbiota in HIV infection – Tiffany Hensley-McBain et al. – PLoS Pathogens

Review: Thinking bigger: How early life environmental exposures shape the gut microbiome and influence the development of asthma and allergic disease – Hind Sbihi et al. – Allergy

** The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight – Francine E. Garrett-Bakelman et al. – Science


Review: Changes in the Human Metabolome Associated With Alcohol Use: A Review – Taija Voutilainen & Olli Kärkkäinen – Alcohol and Alcoholism

Animal microbiome

Dynamic changes in rumen fermentation and bacterial community following rumen fluid transplantation in a sheep model of rumen acidosis: implications for rumen health in ruminants – Junhua Liu et al. – The FASEB Journal

Rainbow trout (Oncorhynchus mykiss) gut microbiota is modulated by insect meal from Hermetia illucens prepupae in the diet – Genciana Terova et al. – Reviews in Fish Biology and Fisheries

Plant, root and soil microbiome

Effects of mycorrhizae and water conditions on perennial ryegrass growth in rare earth tailings – Qiao Yang et al. – RSC Advance

Niche separation of species of entomopathogenic fungi within the genera Metarhizium and Beauveria in different cropping systems in Mexico – J.A. Cabrera-Mora et al. – Fungal Ecology

Soil abiotic properties and plant functional traits mediate associations between soil microbial and plant communities during a secondary forest succession on the Loess Plateau – Yongfu Chai et al. – Frontiers in Microbiology

Microbial Diversity and Antimicrobial Resistance Profile in Microbiota from Soils of Conventional and Organic Farming Systems – Julija Armalytė et al. – Frontiers in Microbiology

Effects of elevated temperature and elevated CO2 on soil nitrification and ammonia-oxidizing microbial communities in field-grown crop – Linh T.T. Nguyen et al. – Science of The Total Environment

Tropical forest conversion to rubber plantation affects soil micro- & mesofaunal community & diversity – Dharmesh Singh et al. – Scientific Reports

Water and extremophile microbiome

Sulfate reduction by a haloalkaliphilic bench-scale sulfate-reducing bioreactor and its bacterial communities at different depths – Tingzhen Mu et al. – Biochemical Engineering Journal

Extremely acidic environment: Biogeochemical effects on algal biofilms – Ana Teresa Luís et al. – Ecotoxicology and Environmental Safety

Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench – Jiwen Liu & Yanfen Zheng et al. – Microbiome

Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges – Rachel Samson et al. – Science of The Total Environment

Distribution of microbial communities in metal-contaminated nearshore sediment from Eastern Guangdong, China – Mei Zhuang et al. – Environmental Pollution

Phages and viruses

Diversities and potential biogeochemical impacts of mangrove soil viruses – Min Jin et al. – Microbiome


Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis – Dongmei Ai et al. – BMC Genomics

Microbes in the news

Can changing the microbiome reverse lactose intolerance? – PATRICIA L. FOSTER – PhillyVoice

A Look at the Trillions of Microorganisms That Live in and on You – Shayla Love – Vice

Mode of delivery alters infants’ gut microbiota and this may impact respiratory health in first year of life – EurekAlert!

Fecal Transplant Reduces Nearly 50 Percent Of Autism Symptoms In Children – Allan Adamson – Tech Times

Edinburgh Science Festival: from gut bacteria and depression to how rice is risking the planet – Helen McArdle – The Herald

Gut microbiome changes emerge as a potential modulator of age-associated cardiovascular disease risk – Andreu Prados – Gut Microbiota for Health

The Gut Microbiome & Cancer Immunotherapy – Osman, Afaf E. G. & Luke, Jason J. – Oncology Times

March 12, 2019

Today’s Digest casts a wide net with focuses on antibiotic resistance , human gut microbiome and microbiome in extreme environments. Highlights include a review on fungi in the marine environment, a report on gut mucosal virome alterations in ulcerative colitis and finally, sleep well!

General microbiology

Review: Transcription in cyanobacteria: a distinctive machinery and putative mechanisms – Amber Riaz-Bradley – Biochemical Society Transactions

Preprint: How sample heterogeneity can obscure the signal of microbial interactions – David W. Armitage & Stuart E. Jones – bioRxiv

Behavioral heterogeneity in quorum sensing can stabilize social cooperation in microbial populations – Kelei Zhao et al. – BMC Biology

Antibiotic resistance

Antimicrobial photodynamic activity of toluidine blue encapsulated in mesoporous silica nanoparticles against Pseudomonas aeruginosa and Staphylococcus aureus – Paramanantham Parasuraman et al. – Biofouling

Metaphire guillelmi gut as hospitable micro-environment for the potential transmission of antibiotic resistance genes – Huizhen Chao et al. – Science of The Total Environment

Abundance of antibiotic resistance genes and their association with bacterial communities in activated sludge of wastewater treatment plants: Geographical distribution and network analysis – Haihan Zhang et al. – Journal of Environmental Sciences

Cationic Intrinsically Disordered Antimicrobial Peptides (CIDAMPs) Represent a New Paradigm of Innate Defense with a Potential for Novel Anti-Infectives – Ties Latendorf et al. – Scientific Reports

Preprint: Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance in a model gut microbiota – Andres Aranda-Diaz et al. – bioRxiv

Human oral microbiome

** Sleep deprivation and a non–24-h working schedule lead to extensive alterations in physiology and behavior – Huan Ma et al. – FASEB J

Human gut microbiome

Review: Microbe-metabolite-host axis, two-way action in the pathogenesis and treatment of human autoimmunity – Xiang Meng et al. – Autoimmunity Reviews

Pearls: Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract – Matthew H. Foley et al. – PLoS Pathogens

Review: Biomarkers for Immune Therapy in Gastrointestinal Cancers – Benjamin A. Weinberg et al. – Clinical Advances in Hematology & Oncology

Microbiota Diversity in Human Colorectal Cancer Tissues Is Associated with Clinicopathological Features – Yaxin Wu et al. – Nutrition and Cancer

Review: The microbiome, cancer, and cancer therapy – Beth A. Helmink et al. – Nature Medicine

Correlations of the Gastric and Duodenal Microbiota with Histological, Endoscopic, and Symptomatic Gastritis – Hye Seung Han et al. – Journal of Clinical Medicine

Gut-microbe-braint axis

Research Highlight: Depression linked to the microbiome – Hannah Stower – Nature Medicine

Animal experiments

Differential Sensitivity to Plasmodium yoelii Infection in C57BL/6 Mice Impacts Gut-Liver Axis Homeostasis – Joshua E. Denny et al. – Scientific Reports

Metabolic footprint and intestinal microbial changes in response to dietary proteins in a pig model – Alexandra Schutkowski et al. – Journal of Nutritional Biochemistry

Alterations of Bile Acids and Gut Microbiota in Obesity Induced by High Fat Diet in Rat Model – Hong Lin et al. – Journal of Agricultural and Food Chemistry

Effects of lifelong intake of lemon polyphenols on aging and intestinal microbiome in the senescence-accelerated mouse prone 1 (SAMP1) – Chikako Shimizu et al. – Scientific Reports

Effect of green tea and mulberry leaf powders on the gut microbiota of chicken – Yuan Chen et al. – BMC Veterinary Research

Animal microbiome

Fiddler crab bioturbation determines consistent changes in bacterial communities across contrasting environmental conditions – Jenny Marie Booth & Marco Fusi et al. – Scientific Reports

Plant, root and soil microbiome

Hypotheses: Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration – Radhey Shyam Sharma et al. – Ecology and Evolution

Native and Invading Yellow Starthistle (Centaurea solstitialis) Microbiomes Differ in Composition and Diversity of Bacteria – Patricia Lu-Irving et al. – mSphere

Small molecule reaction networks that model the ROS dynamics of the rhizosphere – Olga Taran et al. – Chemical Communications

Soil HONO emissions at high moisture content are driven by microbial nitrate reduction to nitrite: tackling the HONO puzzle – Dianming Wu et al. – The ISME Journal

Evidence of within-species specialization by soil microbes and the implications for plant community diversity – Jenalle L. Eck et al. – PNAS

Effects of four years of elevated ozone on microbial biomass and extracellular enzyme activities in a semi-natural grassland – Jinyang Wang et al. – Science of The Total Environment

Water and extremophile microbiome

Surveying of acid-tolerant thermophilic lignocellulolytic fungi in Vietnam reveals surprisingly high genetic diversity – Vu Nguyen Thanh et al. – Scientific Reports

Radioactive environment adapted bacterial communities constituting the biofilms of hydrothermal spring caves (Budapest, Hungary) – Nóra Tünde Enyedi et al. – Journal of Environmental Radioactivity

COD/sulfate ratio does not affect the methane yield and microbial diversity in anaerobic digesters – Zeynep Cetecioglu et al. – Water Research

** Review: Fungi in the Marine Environment: Open Questions and Unsolved Problems – Anthony Amend et al. – mBio

Holocene paleodepositional changes reflected in the sedimentary microbiome of the Black Sea – Kuldeep D. More et al. – Geobiology

Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents – Lucy C. Stewart et al. – The ISME Journal

Prebiotics, probiotics and synbiotics

Review: Potential prebiotics and their transmission mechanisms: Recent approaches – Ishu Khangwal & Pratyoosh Shukla – Journal of Food and Drug Analysis

A Preventive Prebiotic Supplementation Improves the Sweet Taste Perception in Diet-Induced Obese Mice – Arnaud Bernard et al. – Nutrients

Phages and viruses

Pancreas of coxsackie virus infected dams and their challenged pups: A complex issue – Sona Sarmirova et al. – Virulence

Preprint: Clades of huge phage from across Earth’s ecosystems – Basem Al-Shayeb et al. – bioRxiv

** Gut mucosal virome alterations in ulcerative colitis – Tao Zuo et al. – Gut


MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches – Weizhi Song et al. – Microbiome

Scientific Communication and Education

Preprint: The life of P.I. – Transitions to Independence in Academia – Sophie E Acton et al. – bioRxiv

March 5, 2019

A rich Digest for your Tuesday. Microbiome distinguishes atopic dermatitis from allergy, viruses hitchhike insect sperm for paternal transmission, and researchers test biofilms as water quality biosensor. Enjoy!


2017 NIH-wide workshop report on “The Human Microbiome: Emerging Themes at the Horizon of the 21st Century” – The 2017 NIH-wide microbiome workshop writing team – Microbiome

General microbiology

Adaptive laboratory evolution of a genome-reduced Escherichia coli – Donghui Choe et al. – Nature Communications

Frequency of disturbance alters diversity, function, and underlying assembly mechanisms of complex bacterial communities – Ezequiel Santillan et al. – npj Biofilms and Microbiomes

Interactions in self-assembled microbial communities saturate with diversity – Xiaoqian Yu et al. – The ISME Journal

Redox traits characterize the organization of global microbial communities – Salvador Ramírez-Flandes – PNAS

The genetic basis for adaptation of model-designed syntrophic co-cultures – Colton J. Lloyd et al. – PLoS Computational Biology

Antimicrobial resistance

Antibiotic resistance in urban runoff – Ayad Almakki et al. – Science of The Total Environment

Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters – Pablo Fresia et al. – Microbiome

Pregnancy and early life

Longitudinal Microbiome Composition and Stability Correlate with Increased Weight and Length of Very-Low-Birth-Weight Infants – Alyson L. Yee et al. – mSystems

Human skin microbiome

** The nonlesional skin surface distinguishes atopic dermatitis with food allergy as a unique endotype – Donald Y. M. Leung et al. – Science Translational Medicine

Inverse association between the skin and oral microbiota in atopic dermatitis – Wei Li et al. – Journal of Investigative Dermatology

Dysbiosis of skin microbiota in psoriatic patients: co-occurrence of fungal and bacterial communities – Zuzana Stehlikova et al. – Frontiers in Microbiology

Human oral microbiome

Specific Gut and Salivary Microbiota Patterns Are Linked With Different Cognitive Testing Strategies in Minimal Hepatic Encephalopathy – Jasmohan Baja et al. – The American Journal of Gastroenterology

Human respiratory microbiome

A Haemophilus sp. dominates the microbiota of sputum from UK adults with non-severe community acquired pneumonia and chronic lung disease – Daniel G. Wootton et al. – Scientific Reports

Review: The Challenging Road of Moving from Association to Causation for Microbiome Research in IPF – Leopoldo N. Segal & Philip L Molyneaux – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Molecular characterization of multidrug-resistant Pseudomonas aeruginosa isolates in hospitals in Myanmar – Tatsuya Tada et al. – Antimicrobial Agents and Chemotherapy

The Dimension of Time in Host-Microbiome Interactions – Giulia T. Uhr et al. – mSystems

The influence of probiotic bacteria and human gut microorganisms causing opportunistic infections on Blastocystis ST3 – M. Lepczyńska & E. Dzika – Gut Pathogens

Human gut-microbiome-brain axis

Review: Systematic Review of Gut Microbiota and Major Depression – Stephanie G. Cheung et al. – Frontiers in Psychiatry

Human multi-site microbiome

Influences on allergic mechanisms through gut, lung, and skin microbiome exposures – Andrea M. Kemter & Cathryn R. Nagler – The Journal of Clinical Investigation

Animal experiments

Metabolic and gut microbial characterization of obesity-prone mice under high-fat diet – Yu Gu et al. – Journal of Proteome Research

Mouse: Impact of 5 Fluorouracil Chemotherapy on Gut Inflammation, Functional Parameters, and Gut Microbiota – A.T.Sougiannis et al. – Brain, Behavior, and Immunity

Mouse: Antigen-presenting ILC3 regulate T cell–dependent IgA responses to colonic mucosal bacteria – Felipe Melo-Gonzalez et al. – Journal of Experimental Medicine

Animal microbiome

Host plant and population source drive diversity of microbial gut communities in two polyphagous insects – Asher G. Jones et al. – Scientific Reports

Bacterial Community of the Digestive Tract of the European Medicinal Leech (Hirudo verbana) from the Danube River – Saraswoti Neupane et al. – Microbial Ecology

Gut microbiota of the European Brown Hare (Lepus europaeus) – G. L. Stalder et al. – Scientific Reports

Plant, root and soil microbiome

Soil microbial functions are affected by organic matter removal in temperate deciduous forest – François Maillard et al. – Soil Biology and Biochemistry

Warming counteracts grazing effects on the functional structure of the soil microbial community in a Tibetan grassland – Li Tang et al. – Soil Biology and Biochemistry

Soil Bacterial Communities From the Chilean Andean Highlands: Taxonomic Composition and Culturability – Felipe Maza et al. – Frontiers in Bioengineering and Biotechnology

Foliar Application of Vegetal-Derived Bioactive Compounds Stimulates the Growth of Beneficial Bacteria and Enhances Microbiome Biodiversity in Lettuce – Francesca Luziatelli et al. – Frontiers in Plant Science

Creek to Table: Tracking fecal indicator bacteria, bacterial pathogens, and total bacterial communities from irrigation water to kale and radish crops – Sarah M.Allard et al. – Science of The Total Environment

Water and extremophile microbiome

Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments – Adrien Vigneron et al. – mSystems

Diversity, spatial distribution and activity of fungi in freshwater ecosystems – Cécile Lepère​ et al. – PeerJ

Spatial variability of Antarctic surface snow bacterial communities – Lucie A. Malard et al. – Frontiers in Microbiology

Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network – Keith Bouma-Gregson et al. – The ISME Journal

Vertical stratification of bacteria and archaea in sediments of a small boreal humic lake – Antti J Rissanen et al. – FEMS Microbiology Letters

Airborne Microbial Communities at High-Altitude and Suburban Sites in Toyama, Japan Suggest a New Perspective for Bioprospecting – Daisuke Tanaka et al. – Frontiers in Bioengineering and Biotechnology

Coral microbiome diversity reflects mass coral bleaching susceptibility during the 2016 El Niño heat wave – Stephanie G. Gardner et al. – Ecology and Evolution

Phages and viruses

** Viral pathogens hitchhike with insect sperm for paternal transmission – Qianzhuo Mao et al. – Nature Communications

Early respiratory viral infections in infants with cystic fibrosis – Ashley R. Deschamp et al. – Journal of Cystic Fibrosis


** Oxygen-reducing microbial cathodes monitoring toxic shocks in tap water – Antonin Prévoteau et al. – Biosensors and Bioelectronics

Inhibition of methanogens decreased sulfadiazine removal and increased antibiotic resistance gene development in microbial fuel cells – Shuai Zhang et al. – Bioresource Technology

Effect of the extraction and purification of soil DNA and pooling of PCR amplification products on the description of bacterial and archaeal communities – Johan S. Sáenz et al. – Journal of Applied Microbiology

Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling – Zigui Chen et al. – mSystems

Ultrahigh-Throughput Multiplexing and Sequencing of >500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 Platform – Johanna B. Holm et al. – mSystems

Fungal Cells Recovery From Air Samples: A Tale of Loss And Gain – Hamza Mbareche et al. – Applied and Environmental Microbiology


Genome and pan-genome analysis to classify emerging bacteria – Aurélia Caputo et al. – Biology Direct

16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses – Stephen Woloszynek et al. – PLoS Computational Biology