October 23, 2019

A rich Digest today featuring the “Prime Editing” invented by the David R. Liu lab, which promises to correct 89% of point mutations, an ultra-deep metagenomic study of phages in aquatic systems and strain level interaction between bacteria and plants. Enjoy!

General microbiology

** Search-and-replace genome editing without double-strand breaks or donor DNA – Andrew V. Anzalone et al. – Nature

Resolving a piece of the archaeal lipid puzzle – Ann Pearson – PNAS

Antimicrobial resistance

Commentary: Surveillance and monitoring of antimicrobial resistance: limitations and lessons from the GRAM project – Jesse Schnall et al. – BMC Medicine

Preprint: In vitro Efficacy of Novel Glucan Synthase Inhibitor, Ibrexafungerp (SCY-078), Against Multidrug- and Pan-resistant Candida auris Isolates from the Outbreak in New York – Yan Chun Zhu et al. – bioRxiv

Review: Proteomics approach to understand bacterial antibiotic resistance strategies – Bo Peng et al. – Expert Review of Proteomics

Human oral microbiome

Subgingival Microbiota and Longitudinal Glucose Change: The Oral Infections, Glucose Intolerance and Insulin Resistance Study (ORIGINS) – R.T. Demmer et al. – Journal of Dental Research

Human gut microbiome

Review: Systems biology perspective for studying the gut microbiota in human physiology and liver diseases – Ozlem Altay et al. – EBioMedicine

Review: Intestinal microbiota and colorectal carcinoma: Implications for pathogenesis, diagnosis, and therapy – Ana Montalban-Arques & Michael Scharl – EBioMedicine

Perspective: Carbohydrate-based Prebiotics in Targeted Modulation of Gut Microbiome – Ka-Lung Lam & Peter Chi Keung Cheung – Journal of Agricultural and Food Chemistry


Early Detection of Cystic Fibrosis Acute Pulmonary Exacerbations by Exhaled Breath Condensate Metabolomics – Xiaoling Zang et al. – Journal of Proteome Research

Food microbiome

Peer pressure: Evolutionary responses to biotic pressures in wine yeasts – C. G. Conacher et al. – FEMS Yeast Research

Animal experiments

Disruption of gut integrity and permeability contributes to enteritis in a fish-parasite model: a story told from serum metabolomics – Ariadna Sitjà-Bobadilla et al. – Parasites & Vectors

Animal microbiome

Estimating the burden of dengue and the impact of release of wMel Wolbachia-infected mosquitoes in Indonesia: a modelling study – Kathleen M. O’Reilly et al. – BMC Medicine

Plant, root and soil microbiome

Preprint: Insights into the desert living skin microbiome: geography, soil depth, and crust type affect biocrust microbial communities and networks in Mojave Desert, USA – Nuttapon Pombubpa et al. – bioRxiv

** Metabolites in the root exudates of groundnut change during interaction with plant growth promoting rhizobacteria in a strain-specific manner – Sravani Ankati & Appa Rao Podile – Journal of Plant Physiology

Environmental and biotic drivers of soil microbial β-diversity across spatial and phylogenetic scales – Loïc Chalmandrier et al. – Ecography

Soil hydrology drives ecological niche differentiation in a native prairie microbiome – James S Griffin et al. – FEMS Microbiology Ecology

Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species – Julien Massoni et al. – The ISME Journal

Effect of aridity and dune type on rhizosphere soil bacterial communities of Caragana microphylla in desert regions of northern China – Jiangli Gao et al. – PLoS One

Rhizosphere bacterial community in watermelon-wheat intercropping was more stable than in watermelon monoculture system under Fusarium oxysporum f. sp. niveum invasion – Hongjie Yu et al. – Plant and Soil

Phosphorus-acquisition strategies of canola, wheat and barley in soil amended with sewage sludges – C. Nobile et al. – Scientific Reports

Water and extremophile microbiome

Distinctive microbial communities in subzero hypersaline brines from Arctic coastal sea ice and rarely sampled cryopegs – Zachary S. Cooper et al. – FEMS Microbiology Ecology

Performance and microbial communities of different biofilm membrane bioreactors with pre-anoxic tanks treating mariculture wastewater – Huining Zhang et al. – Bioresource Technology

Do organic substrates drive microbial community interactions in Arctic snow? – Benoît Bergk Pinto et al. – Frontiers in Microbiology

Genomic signatures for sedimentary microbial utilization of phytoplankton detritus in a fast-flowing estuary – Mariya W. Smit et al. – Frontiers in Microbiology

pH control and microbial community analysis with HCl or CO2 addition in H2-based autotrophic denitrification – Wei Xing et al. – Water Research

Extremophilic nitrite-oxidizing Chloroflexi from Yellowstone hot springs – Eva Spieck et al. – The ISME Journal

Phages and viruses

** Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics – Vinicius S. Kavagutti et al. – Microbiome

Review: Phage Therapy with a Focus on the Human Microbiota – Sharita Divya Ganeshan & Zeinab Hosseinidoust – Antibiotics


Preprint: Gene copy normalization of the 16S rRNA gene cannot outweigh the methodological biases of sequencing – Robert Starke & Daniel Morais – bioRxiv

Review: Third generation sequencing in the clinical laboratory: Exploring the advantages and challenges of nanopore sequencing – Lauren M. Petersen et al. – Journal Clinical Microbiology

Microbes in the news

Which foods are beneficial for a healthy gut microbiome? – Ana Sandoiu – Medical News Today

Microbiome: Untapped source of novel antimicrobials – Delthia Ricks – Medical Xpress

The Problem With Labeling Gut Troubles ‘Dysbiosis’ – Elizabeth Preston – Undark

Bacteria for beauty: why you need to start thinking about your skin microbiome – Hannah Ebelthite – Telegraph

Research Finds These Mediterranean Diet Foods Protect The Gut Microbiome – Jamie Schneider – Mind Body Green

Are undiscovered antibiotics ‘silently waiting’ in our own bodies? Researchers scour microbiome for helpful genes – Shelly Fan – Genetic Literacy Project

Reprogramming the microbiome: Antara Lifesciences targets the human health space with dual targeted formulation – Tingmin Koe – Food Navigator Asia

Transient and long-term disruption of gut microbes after antibiotics – Jeff Hansen – UAB News

Microbes on the market

Microba, Psomagen Partner to Launch Microbiome Test in US – GenomeWeb

October 9, 2019

Today’s Digest includes plenty of human gut microbiome papers, and plant, soil, water microbiome papers. Today features a major expansion of human gut MAGs, evolution of human gut microbiome compared with apes, and how soil microbiome affects climate change and vice versa. A potentially revolutionary technology promises to finally bring microbiome dark matters into daylight, and don’t forget to check out our own Elies Bik’s excellent work on exposing scientific fraud! Enjoy.

General microbiology

Tradeoffs in hyphal traits determine mycelium architecture in saprobic fungi – Anika Lehmann et al. – Scientific Reports

Review: Nature’s recyclers: anaerobic microbial communities drive crude biomass deconstruction – Stephen P Lillington et al. – Current Opinion in Biotechnology

Review: Microbial functional diversity: From concepts to applications – Arthur Escalas e t al. – Ecology and Evolution

Antimicrobial resistance

Preprint: Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: An inter-laboratory study – Ronan M Doyle et al. – bioRxiv

Human gut microbiome

** Preprint: A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome – Alexandre Almeida et al. – bioRxiv

** Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny – Katherine R. Amato et al. – Genome Biology

Press: New research furthers understanding about what shapes human gut microbiome – EurekAlert!

Review: Sodium, Hypertension, and the Gut: Does the Gut Microbiota Go Salty? – Katarina Smiljanec & Shannon L. Lennon – American Journal of Physiology-Heart and Circulatory Physiology

Tea Compounds and the Gut Microbiome: Findings from Trials and Mechanistic Studies – Timothy Bond & Emma Derbyshire – Nutrients

Fecal microbiota and metabolites are distinct in a pilot study of pediatric Crohn’s disease patients with higher levels of perceived stress – Laura M. Mackner et al. – Psychoneuroendocrinology

Review: The Gut Microbiota in Celiac Disease and probiotics – Richa Chibbar & Levinus A. Dieleman – Nutrients

Systemic Lupus Erythematosus and dysbiosis in the microbiome: cause or effect or both? – Gregg J Silverman et al. – Current Opinion in Immunology

Review: The Multiple Sclerosis Gut Microbiota: A Systematic Review – Ali Mirza et al. – Multiple Sclerosis and Related Disorders

Animal experiments

Oolong tea polyphenols ameliorate circadian rhythm of intestinal microbiome and liver clock genes in mouse model – Tongtong Guo et al. – Journal of Agricultural and Food Chemistry

Review: Caenorhabditis elegans: a model to understand host–microbe interactions – Arun Kumar et al. – Cellular and Molecular Life Sciences

Animal microbiome

Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales – Candace L. Williams et al. – Drug Discovery Today: Disease Models

Plant, root and soil microbiome

Soil Microbial Communities Involved in Reductive Dissolution of Arsenic from Arsenate-laden Minerals with Different Carbon Sources – Shigeki Yamamura et al. – Environmental Science & Technology

Volatile‐mediated antagonism of soil bacterial communities against fungi – Xiaogang Li et al. – Environmental Microbiology

Interactions between soybean, Bradyrhizobium japonicum and Soybean mosaic virus: the effects depend on the interaction sequence – Sofía Andreola et al. – Functional Plant Biology

New insights into the responses of soil microorganisms to polycyclic aromatic hydrocarbon stress by combining enzyme activity and sequencing analysis with metabolomics – Xiaona Li et al. – Environmental Pollution

Understanding the phyllosphere microbiome assemblage in grape species (Vitaceae) with amplicon sequence data structures – Prashant Singh et al. – Scientific Reports

** Review: Soil microbiomes and climate change – Janet K. Jansson & Kirsten S. Hofmockel – Nature Reviews Microbiology

Variation in pickleweed root-associated microbial communities at different locations of a saline solid waste management unit contaminated with petroleum hydrocarbons – Abdur Rahim Khan et al. – PLoS One

Plant-plant competition influences temporal dynamism of soil microbial enzyme activity – E. J. Schofield et al. – Soil Biology and Biochemistry

Comparison of microphototrophic communities living in different soil environments in the High Arctic – Ekaterina Pushkareva et al. – Frontiers in Ecology and Evolution

Water and extremophile microbiome

Novel facultative Methylocella strains are active methane consumers at terrestrial natural gas seeps – Muhammad Farhan Ul Haque et al. – Microbiome

Selective bacterial colonization processes on polyethylene waste samples in an abandoned landfill site – Edoardo Puglisi et al. – Scientific Reports

Variation in pickleweed root-associated microbial communities at different locations of a saline solid waste management unit contaminated with petroleum hydrocarbons – Abdur Rahim Khan et al. – PLoS One

Bacterial and Fungal Diversity Inside the Medieval Building Constructed with Sandstone Plates and Lime Mortar as an Example of the Microbial Colonization of a Nutrient-Limited Extreme Environment (Wawel Royal Castle, Krakow, Poland) – Magdalena Dyda et al. – Microorganisms

Evaluating the effect of biochar on mesophilic anaerobic digestion of waste activated sludge and microbial diversity – Bo Wu et al. – Bioresource Technology

Species-specific differences in the microbiomes and organic exudates of crustose coralline algae influence bacterioplankton communities – Zachary A. Quinlan et al. – Frontiers in Microbiology

A global comparison of the bacterial communities of bilge water, boat surfaces, and external port water – Laura G. Schaerer et al. – Applied and Environmental Microbiology

Microbes in space

Simulated manned Mars exploration: effects of dietary and diurnal cycle variations on the gut microbiome of crew members in a controlled ecological life support system – Hai-Sheng Dong et al. – PeerJ


** Targeted isolation and cultivation of uncultivated bacteria by reverse genomics – Karissa L. Cross et al. – Nature Biotechnology


Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases – Ole K Tørresen et al. – Nucleic Acids Research

Microbes in the news

Bill Gates thinks understanding the body’s microbiome will help solve malnutrition – Katie Palmer – Quartz

Press for yesterday’s article: Unlocking CRISPR’s Potential To Alter the Microbiome – Technology Networks

Press for yesterday’s article: New Study Finds CRISPR May Be The Secret To Improving Gut Health – Gretchen Lidicker – Mind Body Green

Drug Metabolism and Microbiome – Maryam Azizi – News Medical

The Gut-Lupus Link: How Gut Bacteria May Impact Disease Development and Activity – Lupus Foundation of America

Microbes on the market

BASF and Biomillenia Join Forces in Microbiome Research to Promote Healthy Skin – Business Wire

Non-microbiology pick

** Our own Elies Bik is featured in this Dutch report on exposing scientific fraud, and see a Google translated version here.

September 11, 2019

Today’s Digest features a study on how antibiotic use in preterm infants might cause long-term impacts, a report on the effect of antibiotics on vaccine response, and a special issue on microbiome biology. Happy reading!


Nutrition and Health: Human Microbiome – a MOOC by Clara Belzer – Gut Microbiota For Health

General microbiome

** Special Issue: Microbiome Biology – Genome Biology & BMC Biology

Editorial: Expanding the scope and scale of microbiome research – Rob Knight et al. – Genome Biology

Review: Challenges in the construction of knowledge bases for human microbiome-disease associations – Varsha Dave Badal et al. – Microbiome

Review: The Microbiome and Aging – Bianca Bana & Filipe Cabreiro – Annual Review of Genetics

Pregnancy and early life

** Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome – Andrew J. Gasparrini et al. – Nature Microbiology

Press: Prolonged antibiotic treatment may alter preterm infants’ microbiome – National Institutes of Health

Review: Maternal Microbiome and Metabolic Health Program Microbiome Development and Health of the Offspring – Marta Calatayud et al. – Trends in Endocrinology & Metabolism

Human respiratory microbiome

In vitro: In vitro evolution of Pseudomonas aeruginosa AA2 biofilms in the presence of cystic fibrosis lung microbiome members – Eva Vandeplassche et al. – Scientific Reports

Human gut microbiome

** Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans – Thomas Hagan et al. – Cell

Press: Microbiome loss from antibiotic use affects response to flu vaccine – Angela Betsaida B. Laguipo – News Medical

Predictors of Obesity among Gut Microbiota Biomarkers in African American Men with and without Diabetes – Elena Barengolts et al. – Microorganisms

Protocol: Prospective multicentre cohort trial on acute appendicitis and microbiota, aetiology and effects of antimicrobial treatment: study protocol for the MAPPAC (Microbiology APPendicitis ACuta) trial – Sanja Vanhatalo et al. – BMJ Open

Effects of anti-H. pylori triple therapy and a probiotic complex on intestinal microbiota in duodenal ulcer – Lili Wu et al. – Scientific Reports

Cancer microbiome

Review: The Microbiome and Prostate Cancer Risk – Karen M. Wheeler & Michael A. Liss – Current Urology Reports

Press: The Microbiome and Prostate Cancer Risk – Uro Today

Profiling of lung microbiota discloses differences in adenocarcinoma and squamous cell carcinoma – Sílvia Gomes et al. – Scientific Reports

Animal experiments

Triclosan-selected host-associated microbiota perform xenobiotic biotransformations in larval zebrafish – Chelsea A Weitekamp et al. – Toxicological Sciences

Effects of theabrownin on serum metabolite and gut microbiome in rats with high-sugar diet – Suijuan Yue et al. – Food & Function

Animal microbiome

Effects of long-term starvation on health indices, gut microbiota and innate immune response of fresh water crayfish, marron (Cherax cainii, Austin 2002) – Md Javed Foysal et al. – Aquaculture

Plant, root and soil microbiome

Effects of road salt on microbial communities: Halophiles as biomarkers of road salt pollution – Wolf T. Pecher et al. – PLoS One

Conservation of the endophyte microbiome structure across two Panicum grass species – Esther Singer et al. – Frontiers in Microbiology

Characterization of Microbial Communities, Identification of Cr(VI) Reducing Bacteria in Constructed Wetland and Cr(VI) Removal Ability of Bacillus cereus – Hua Lin et al. – Scientific Reports

Review: The plant microbiome: A missing link for the understanding of community dynamics and multifunctionality in forest ecosystems – Sandhya Mishra e al. – Applied Soil Ecology

Combining irrigation scheme and phosphorous application levels for grain yield and their impacts on rhizosphere microbial communities of two rice varieties in a field trial – Yingjiao Zhang et al. – Journal of Agricultural and Food Chemistry

Soil-plant compartments affect fungal microbiome diversity and composition in grapevine – María del PilarMartínez-Diz et al. – Fungal Ecology

Water and extremophile microbiome

The fungicide azoxystrobin promotes freshwater cyanobacterial dominance through altering competition – Tao Lu et al. – Microbiome

Diel oscillation of microbial gene transcription declines with increasing depth in oligotrophic ocean waters – Alice Vislova et al. – Frontiers in Microbiology

Long term performance and dynamics of microbial biofilm communities performing sulfur-oxidizing autotrophic denitrification in a moving-bed biofilm reactor – Yan-Xiang Cui et al. – Water Research

Opportunistic pathogens and large microbial diversity detected in source-to-distribution drinking water of three remote communities in Northern Australia – Mirjam Kaestli et al. – PLoS Neglected Tropical Diseases

The diversity and biogeography of microeukaryotes in the euphotic zone of the northwestern Pacific Ocean – Peng-Fei Wu et al. – Science of the Total Environment

Comparative evaluation of three archaeal primer pairs for exploring archaeal communities in deep-sea sediments and permafrost soils – Shiping Wei et al. – Extremophiles

Characterizations of microbial diversity and machine oil degrading microbes in machine oil contaminated soil – Mengjiao Wang et al. – Environmental Pollution

Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes – Molly P. Mikan et al. – The ISME Journal

Microbes in space

Space Station conditions are selective but do not alter microbial characteristics relevant to human health – Maximilian Mora et al. – Nature Communications

Phages and viruses

Preprint: European and tropical Aedes albopictus mosquito populations have similar systemic Zika virus infection dynamics – Sebastian Lequime et al. – bioRxiv


Preprint: A novel and direct mobilome approach improves the detection of larger-sized circular elements across kingdoms – Katrine Skov Alanin et al. – bioRxiv

Power production and microbial community composition in thermophilic acetate-fed up-flow and flow-through microbial fuel cells – Paolo Dessì et al. – Bioresource Technology

Microbial Interaction Network Inference in Microfluidic Droplets – Ryan H. Hsu et al. – Cell Systems

Revealing the metabolic capacity of Streblomastix strix and its bacterial symbionts using single-cell metagenomics – Sebastian C. Treitli et al. – PNAS


Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data – Emiliano Pereira-Flores et al. – BMC Bioinformatics

Microbes in the news

The diet-microbiome connection in inflammatory bowel disease – University of Pennsylvania – EurekAlert!

How Bacteria Rule Over Your Body – The Microbiome – YouTube

Will Drinking Red Wine Give You A Healthier Microbiome? – Angela Dowden – American Council on Science and Health

What Role Does Bariatric Surgery Play in Altering the Gut Microbiome? – Suzanne Bujara – Endocrinology Advisor

Microbes on the market

Poised for growth: how to scale a microbiome engineering company – Embriette Hyde – SynbioBeta

September 6, 2019

Today’s rich Digest features a report on how persister pathogens can spread antibiotic resistant plasmids, a study on how diet might alleviate Alzheimer’s, and a screen for the effect of microbiome on diabetes drug efficacy. Other highlights include the evolution and ecology of animal gut microbial communities, microbial communities in soils with radioactive contamination, and free microbiome standards by Zymo Research. Happy reading!

General microbiology

The horizontal gene transfer of Agrobacterium T-DNAs into the series Batatas (Genus Ipomoea) genome is not confined to hexaploid sweetpotato – Dora G. Quispe-Huamanquispe et al. – Scientific Reports

Simulations reveal challenges to artificial community selection and possible strategies for success – Li Xie et al. – PLoS Biology

Primer: Artificially selecting microbial communities: If we can breed dogs, why not microbiomes? – Flor I. Arias-Sánchez et al. – PLoS Biology

Antimicrobial resistance

** Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut – Erik Bakkeren et al. – Nature

Pregnancy and early life

Prenatal antibiotics exposure and the risk of autism spectrum disorders: A population-based cohort study – Amani F. Hamad et al. – PLoS One

Visualization of microbes by 16S in situ hybridization in term and preterm placentas without intraamniotic infection – Maxim D. Seferovic et al. – AJOG

Fetal exposure to the maternal microbiota in humans and mice – Noelle Younge et al. – JCI Insight

Fungi form interkingdom microbial communities in the primordial human gut that develop with gestational age – Kent A. Willis et al. – FASEB J.

Human oral and esophageal microbiome

In vitro: The inhibitory effect of quaternary ammonium salt on bacteria in root canal – Sanjay Kumar Tiwari et al. – Scientific Reports

Alterations to the Esophageal Microbiome Associated with Progression from Barrett’s Esophagus to Esophageal Adenocarcinoma – Erik J. Snider et al. – Cancer Epidemiology, Biomarkers & Prevention

Human respiratory microbiome

Review: The microbiome in bronchiectasis – Hollian Richardson et al. – European Respiratory Review

Human gut microbiome

Gut microbiota alterations associated with reduced bone mineral density in older adults – Mrinmoy Das et al. – Rheumatology

Press: Confounding factors in the effect of gut microbiota on bone density – Rajeev Aurora – Rheumatology

Characterization of Proximal Small Intestinal Microbiota in Patients With Suspected Small Intestinal Bacterial Overgrowth – Andrea S. Shin et al. – Clinical and Translational Gastroenterology

Gut microbiota shifts in patients with gastric cancer in perioperative period – Liang, Weiren et al. – Medicine

Human gut-microbiome-brain axis

** Modified Mediterranean-ketogenic diet modulates gut microbiome and short-chain fatty acids in association with Alzheimer’s disease markers in subjects with mild cognitive impairment – Ravinder Nagpal et al. – EBioMedicine

Press: Diet’s effect on gut bacteria could play role in reducing Alzheimer’s risk – Science Daily

Systemic review and meta-analysis of alcohol induced gut dysbiosis and the resulting behavioral impact – Nayab Qamar et al. – Behavioral Brain Research

Review: The Microbiota-Gut-Brain Axis – John F. Cryan et al. – Physiological Reviews

Human multi-site microbiome

Prosthetic joint infections present diverse and unique microbial communities using combined whole-genome shotgun sequencing and culturing methods – Abigail A. Weaver et al. – Journal of Medical Microbiology


Metabolic switches from quiescence to growth in synchronized Saccharomyces cerevisiae – Jinrui Zhang et al. – Metabolomics

Animal experiments

Dietary inulin alters the gut microbiome, enhances systemic metabolism and reduces neuroinflammation in an APOE4 mouse model – Jared D. Hoffman et al. – PLoS One

Beneficial roles of probiotics on the modulation of gut microbiota and immune response in pigs – Donghyun Shin et al. – PLoS One

Effects of antibacterial peptides on rumen fermentation function and rumen microorganisms in goats – Zhihua Ren et al. – PLoS One

** Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin Therapy – Rosina Pryor et al. – Cell

Press: An Elegan(t) screen shows how the microbiome improves drug efficacy – MRC Research News

Rat: Variation in the gut microbial community is associated with the progression of liver regeneration – Qiongling Bao et al. – Hepatology Research

Animal microbiome

The Pacific harbor seal gut microbiota in Mexico: Its relationship with diet and functional inferences – Arlette Pacheco-Sandoval et al. – PLoS One

Gut microbiota features associated with Clostridioides difficile colonization in puppies – Alexander S. F. Berry et al. – PLoS One

Gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of Nepal – Dibesh Karmacharya et al. – PLoS One

Cadmium and selenate exposure affects the honey bee microbiome and metabolome, and bee-associated bacteria show potential for bioaccumulation – Jason A. Rothman et al. – Applied and Environmental Microbiology

* Review: Evolutionary and Ecological Consequences of Gut Microbial Communities – Nancy A. Moran et al. – Annual Reviews of Ecology, Evolution & Systemactics

Defining the distinct skin and gut microbiomes of the northern pike (Esox lucius) – Elizabeth M. Reinhart et al. – Frontiers in Microbiology

Predicting the unpredictable: How host specific is the mycobiota of bark and ambrosia beetles? – Kirsten E. Miller et al. – Fungal Ecology

Plant, root and soil microbiome

Preprint: The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts – Avihai Zolti et al. – bioRxiv

Soil indigenous microbiome and plant genotypes cooperatively modify soybean rhizosphere microbiome assembly – Fang Liu et al. – BMC Microbiology

* Community structure and functional genes in radionuclide contaminated soils in Chernobyl and Fukushima – Carolina Hoyos-Hernandez et al. – FEMS Microbiology Letters

Microalgae and phototrophic purple bacteria for nutrient recovery from agri-industrial effluents: Influences on plant growth, rhizosphere bacteria and putative carbon and nitrogen cycling genes – Somayeh Zarezadeh et al. – Frontiers in Plant Science

Shifts and recovery of soil microbial communities in a 40-year field trial under mineral fertilization – Jiří Čuhel et al. – Pedobiologia

Water and extremophile microbiome

Identification of soluble microbial products (SMPs) from the fermentation and methanogenic phases of anaerobic digestion – C. Kunacheva et al. – Science of the Total Environment

Review: Microbial mercury methylation in the cryosphere: Progress and prospects – Prakriti Sharma Ghimire et al. – Science of the Total Environment

Rapid Colonization of Uranium Mining-Impacted Waters, the Biodiversity of Successful Lineages of Phytoplankton Extremophiles – Beatriz Baselga-Cervera – Microbial Ecology

Relationship between microbial community and environmental conditions in a constructed wetland system treating greywater – F.S.Bernardes et al. – Ecological Engineering

Built environment microbiome

Microbial Exchange via Fomites and Implications for Human Health – Brent Stephens et al. – Current Pollution Reports

Phages and viruses

Faecal Virome Analysis of Wild Animals from Brazil – Matheus A. Duarte et al. – Viruses


Accurate estimation of microbial sequence diversity with Distanced – Timothy J Hackmann – Bioinformatics

Microbes in the news

Researchers reveal how bacteria behind hospital infections block out antibiotics – Dumbarton and Vale of Leven Reporter

Using mouthwash could reduce benefits of exercise – Dumbarton and Vale of Leven Reporter

A comprehensive catalogue of human digestive tract bacteria – Anne Trafton – MIT News

No poop required: Researchers devise blood test for gut microbiome diversity using data from defunct startup Arivale – James Thorne – Geek Wire

* Zymo Research Distributes Free Microbiome Standards and Controls – PR Newswire

Top List: Trending in microbiome: From comprehensive culture workflows, to novel biotherapeutics, and microbial characterization – Select Science

APC Researcher Awarded Global Grant For Gut Health – APC Microbiome Ireland

* Poop-testing startup uBiome was once valued at $600 million by Silicon Valley’s top VCs. It just filed for bankruptcy – Erin Brodwin & Emma Court – Business Insider

Gut feeling: How a healthy microbiome helps beat stress and lift mood – Scott Anderson – New Scientist

HLA Alleles With Risk for Ankylosing Spondylitis, Rheumatoid Arthritis Affect Gut Microbiome – Hannah Dellabella – Rheumatology Advisor

How the microbiome movement can be beneficial to you overall health – KUSI Newsroom

No microbiome is an island, survey reveals – Elizabeth Pennisi – Science

Microbes on the market

Metagenomic Analysis of the Human Microbiome – Technology Networks

Update note: Added additional pregnancy/neonatal microbiome papers – Sept 15, @kentmd

August 22, 2019

Today’s Digest includes several papers on antimicrobial resistance, which is what we should be thinking about all the time. Other highlights include nanoparticle delivered medicine for colitis, and how ants compartmentalize microbiomes. Enjoy reading!


Call for papers: Microbiome in human physiological function – Microbial Cell Factories

General microbiology

Species matter for predicting the functioning of evolving microbial communities – An eco-evolutionary model – Timothy G. Barraclough – PLoS One

Antimicrobial resistance

The impact and mechanism of quaternary ammonium compounds on the transmission of antibiotic resistance genes – Yue Han et al. – Environmental Science and Pollution Research

Characterizing the soil microbiome and quantifying antibiotic resistance gene dynamics in agricultural soil following swine CAFO manure application – Edward Lopatto et al. – PLoS One

Antibiotic resistant bacteria and commensal fungi are common and conserved in the mosquito microbiome – Josephine Hyde et al. – PLoS One

Advanced neonatal medicine in China: Is newborn ward capacity associated with inpatient antibiotic usage? – Yi Ge et al. – PLoS One

Preprint: Resident microbial communities inhibit growth and antibiotic resistance evolution of Escherichia coli in human gut microbiome samples – Michael Baumgartner et al. – bioRxiv

Human gut microbiome

** Hyaluronic acid–bilirubin nanomedicine for targeted modulation of dysregulated intestinal barrier, microbiome and immune responses in colitis – Yonghyun Lee et al. – Nature Materials

Press: Nanoparticle relieved symptoms of inflammatory bowel disease in mice – Phys.org

Genetic risk for autoimmunity is associated with distinct changes in the human gut microbiome – Jordan T. Russell et al. – Nature Communications

Preprint: In vitro modeling: Evidence for a multi-level trophic organization of the human gut microbiome – Tong Wang et al. – bioRxiv

Animal microbiome

Relationships between feeding and microbial faeces indices in dairy cows at different milk yield levels – Stephanie Meyer et al. – PLoS One

** Azteca ants maintain unique microbiomes across functionally distinct nest chambers – Jane M. Lucas et al. – Proceedings of the Royal Society B

Press: For at Least One Species, Ant Nurseries Are Cleaner Than Human Ones – Matt Shipman – NC State University

Unveiled feather microcosm: feather microbiota of passerine birds is closely associated with host species identity and bacteriocin-producing bacteria – Veronika Gvoždíková Javůrková et al. – The ISME Journal

Variability in snake skin microbial assemblages across spatial scales and disease states – Donald M. Walker et al. – The ISME Journal

Food microbiome

Faecalibacterium diversity in dairy cow milk – Keith W. Savin et al. – PLoS One

Plant, root and soil microbiome

Microbial succession on decomposing root litter in a drought-prone Scots pine forest – Claude Herzog et al. – The ISME Journal

Water and extremophile microbiome

Active subseafloor microbial communities from Mariana back-arc venting fluids share metabolic strategies across different thermal niches and taxa – Elizabeth Trembath-Reichert, David A. Butterfield & Julie A. Huber – The ISME Journal

Phages and viruses

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes – Simon Roux et al. – Nature Microbiology

Sources of Airborne Norovirus in Hospital Outbreaks – Malin Alsved et al. – Clinical Infectious Diseases

Viral taxonomy derived from evolutionary genome relationships – Tyler J. Dougan & Stephen R. Quake – PLoS One

Microbes in the news

Type 1 diabetes: Genetic risk reflected in gut microbiome – Ana Sandoiu – Medical News Today

10 Things Viome’s Gut Test Can Reveal About Your Gut Microbiome – Yahoo! Finance

Stanford Team Uses Imputation Approach to Uncover Thousands of New Microbiome Proteins – Neil Versel – Genome Web

Broccoli Is Dying. Corn Is Toxic. Long Live Microbiomes! – Louise Elizabeth Maher-Johnson & Ayana Elizabeth Johnson – Scientific American

A mother’s microbes may be a signifier of her child’s future health, researchers say – Michael Eisenstein – Medical Xpress

Pharmacomicrobiomic Study Shows Significant Gut Bacteria Role in Drug Metabolism and Exposure – Kristiana A. Avad & Kirk E. Hevener – Contagion Live

3 Reasons Eliminating Grains May Be Harmful For Gut Health – Jason Wachob – Mind Body Green

Levofloxacin Prophylaxis Least Disruptive to Gut Microbiome in Patients With Hematologic Malignancy – Sweta Gupta – Infectious Disease Advisor

August 8, 2019

Today’s Digest brings you plenty of articles and news pieces, and highlights include mouse experiments with humanized microbiota, with “wilding” microbiota, and a collection of rumen metagenomes. Enjoy reading!


The Expert Is In: Magnetic bacteria pumping iron! – National Museum of Natural History – August 9, 11am-1pm EDT

Antimicrobial resistance

Random peptide mixtures entrapped within a copper-cuprite matrix: new antimicrobial agent against methicillin-resistant Staphylococcus aureus – Tal Stern Bauer et al. – Scientific Reports

ABC Transporter Genes Show Upregulated Expression in Drug-Resistant Clinical Isolates of Candida auris: A Genome-Wide Characterization of ATP-Binding Cassette (ABC) Transporter Genes – Mohd Wasi, Nitesh Kumar Khandelwal & Alexander J. Moorhouse et al. – Frontiers in Microbiology

Preprint: Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance – David C. Danko et al. – bioRxiv

Antimicrobial use in an Indonesian community cohort 0-18 months of age – Jarir At Thobari et al. – PLoS One

Erythromycin-resistant lactic acid bacteria in the healthy gut of vegans, ovo-lacto vegetarians and omnivores – Vesna Milanović et al. – PLoS One

Pregnancy and early life

Predictive value of cervical cytokine, antimicrobial and microflora levels for pre-term birth in high-risk women – Rashmi Manning et al. – Scientific Reports

Human multi-site microbiome

A new issue of the Gastroenterology Clinics of North America

Human oral microbiome

Review: Oral microbial biofilms: an update – Seyed Ali Mosaddad et al. – European Journal of Clinical Microbiology & Infectious Diseases

Amplicon-based microbiome study highlights the loss of diversity and the establishment of a set of species in patients with dentin caries – Diana Wolff et al. – PLoS One

Microbiome in maintained periodontitis and its shift over a single maintenance interval of three months – Hongye Lu et al. – Journal of Clinical Periodontology

Human gut microbiome

Review: Role of microbes, metabolites and effector compounds in host–microbiota interaction: a pharmacological outlook – Bharat Bhushan et al. – Environmental Chemistry Letters

Age-Associated Changes in Gut Microbiota and Dietary Components Related with the Immune System in Adulthood and Old Age: A Cross-Sectional Study – Nuria Salazar et al. – Nutrients

Review: Establishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future Directions – Michael I McBurney et al. – The Journal of Nutrition

Review: Gut Dysbiosis and the Intestinal Microbiome: Streptococcus thermophilus a Key Probiotic for Reducing Uremia – Luis Vitetta et al. – Microorganisms

Animal experiments

** Baseline microbiota composition modulates antibiotic-mediated effects on the gut microbiota and host – Aonghus Lavelle et al. – Microbiome

Microbiota of newborn calves and their mothers reveals possible transfer routes for newborn calves’ gastrointestinal microbiota – Daniela Klein-Jöbstl et al. – PLos One

Isoorientin attenuates benzo[a]pyrene-induced colonic injury and gut microbiota disorders in mice – Shenyuan He et al. – Food Research International

** Laboratory mice born to wild mice have natural microbiota and model human immune responses – Stephan P. Rosshart et al. – Science

Antibiotic-Induced Perturbations Are Manifested in the Dominant Intestinal Bacterial Phyla of Atlantic Salmon – Shruti Gupta et al. – Microorganisms

Whole Body Vibration-Induced Omental Macrophage Polarization and Fecal Microbiome Modification in a Murine Model – Jack C. Yu et al. – International Journal of Molecular Sciences

Press: Whole body vibration shakes up microbiome, reduces inflammation in diabetes – EurekAlert

Press: Whole body vibration helps reduce inflammation, thanks to the gut microbiome – Angela Betsaida B. Laguipo – News-Medical

Animal microbiome

Sex-specific linkages between taxonomic and functional profiles of tick gut microbiomes – Dasiel Obregón et al. – Frontiers in Cellular and Infection Microbiology

** Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery – Robert D. Stewart et al. – Nature Biotechnology

Humoral immune responses against gut bacteria in dogs with inflammatory bowel disease – Sirikul Soontararak et al. – PLoS One

Plant, root and soil microbiome

Solarization-based pesticide degradation results in decreased activity and biomass of the soil microbial community – M.Díaz-López et al. – Geoderma

Soil microbial carbon metabolism reveals a disease suppression pattern in continuous ginger mono-cropping fields – Xiaojiao Liu et al. – Applied Soil Ecology

Influence of 2,4-D residues on the soil microbial community and growth of tree species – Luciana Monteiro Aguiar et al. – International Journal of Phytoremediation

A Microbiome Study Reveals Seasonal Variation in Endophytic Bacteria Among different Mulberry Cultivars – Ting Ou et al. – Computational and Structural Biotechnology Journal

Biological Soil Crusts from Different Soil Substrates Harbor Distinct Bacterial Groups with the Potential to Produce Exopolysaccharides and Lipopolysaccharides – Barbara Cania et al. – Microbial Ecology

Water and extremophile microbiome

A snapshot of microbial community structures in 20 different field-scale anaerobic bioreactors treating food waste – Seung Gu Shin et al. – Journal of Environmental Management

Microbial uptake kinetics of dissolved organic carbon (DOC) compound groups from river water and sediments – Francesca L. Brailsford et al. – Scientific Reports

Biological removal of selenate in saline wastewater by activated sludge under alternating anoxic/oxic conditions – Yuanyuan Zhang et al. – Frontiers of Environmental Science & Engineering

Built environment microbiome

Environmental factors influencing fungal growth on gypsum boards and their structural biodeterioration: A university campus case study – Negin Kazemian et al. – PLoS One

Phages and viruses

Identification of diverse bat alphacoronaviruses and betacoronaviruses in China provides new insights into the evolution and origin of coronavirus-related diseases – Yelin Han et al. – Frontiers in Microbiology

The respiratory microbiota: Associations with influenza symptomatology and viral shedding – Kyu Han Lee et al. – Annals of Epidemiology


Review: Simultaneous improving nitrogen removal and decreasing greenhouse gas emission with biofilm carriers addition in ecological floating bed – Shanshan Sun et al. – Bioresource Technology

Comparative evaluation of a novel recombinase polymerase amplification-lateral flow dipstick (RPA-LFD) assay, LAMP, conventional PCR, and leaf-disc baiting methods for detection of Phytophthora sojae – Tingting Dai et al. – Frontiers in Microbiology

Review: Emerging molecular techniques for studying microbial community composition and function in microbiologically influenced corrosion – Susmitha Purnima Kotu et al. – International Biodeterioration & Biodegradation

Microbes in the news

Phase Genomics’ Platform Links Viruses and Antibiotic Resistance Genes to the Microbiome in Study of a Highly Complex Microbial Community – Phase Genomics – Globe Newswire

Mouse Genetics Shape the Gut Microbiome More than Their Environment – Nicoletta Lanese – The Scientist


NEWSProbiotics brand Life Space celebrates the wonder of the human microbiome – Zoe Wilkinson – Mumbrella

Caveats and clinical implications in the connection between the duodenal microbiome, diet and functional gastrointestinal symptoms – Gut Microbiota for Health

The many modes of microbial magic – Giuliana Viglione – Chemical & Engineering News

The secret lives of microbes – ANNEMIEKE VAN ROEKEL – Euro Scientist

IIT develops state-of-art device to detect bacteria – The Pioneer

The Germiest Places in Your Child’s School – Alex Watt – Red Book

Teresa van Dongen’s Mud Well light uses microorganisms to create electricity – Rima Sabina Aouf – De Zeen

Microbes on the market

Shoreline Biome Announces International Distribution Partnerships – Yahoo Finance

What are the prospects for microbiome skin care in Asia? – Simon Pitman – Cosmetics Design – Europe

Biotech startup joins quest to harness microbiome to untether reliance on antibiotics in women’s health – Natalie Grover – Endpoints News

PanTheryx funding will help intensify growth in animal microbiome-focused products – Joseph Harvey – Informa

July 24, 2019

Welcome back! Today’s all-around Digest features an animal study identifying a single bacterium as therapy against rheumatoid arthritis, a field trial with bacteria colonizing and sterile Asian tiger mosquitoes to combat vector borne diseases, and a non-microbiology pick about the balance between longevity and immunity. Enjoy!


Microbiome Movement – Oncology Response Summit – Boston

General microbiology

Motile curved bacteria are Pareto-optimal – Rudi Schuech et al. – PNAS

Press: ‘Curvy bacteria’ weigh the benefits of different shapes – Science Daily

Antimicrobial resistance

The burden of antimicrobial resistance at tertiary care hospital, southern Ethiopia: a three years’ retrospective study – Tsegaye Alemayehu et al. – BMC Infectious Diseases

Human oral microbiome

Review: Regulation of oral immune tolerance by the microbiome in food allergy – Emmanuel Stephen-Victor & Talal A Chatila – Current Opinion in Immunology

Human respiratory microbiome

Editorial: Changes in lung microbiome do not explain the development of ventilator-associated pneumonia – Lieuwe D. J. Bos & Andre C. Kalil – Intensive Care Medicine

Human gut microbiome

In vitro: Microbial communities in a dynamic in vitro model for the human ileum resemble the human ileal microbiota – Maria Stolaki et al. – FEMS Microbiology Ecology

Fecal Microbiota Transplantation in Pouchitis: Clinical, Endoscopic, Histologic, and Microbiota Results from a Pilot Study – Daniel Selvig et al. – Digestive Diseases and Sciences

Dysbiosis of the gut microbiome is associated with CKD5 and correlated with clinical indices of the disease: a case–controlled study – Yang Li et al. – Journal of Translational Medicine

Animal experiments

Supplementation of diet with non-digestible oligosaccharides alters the intestinal microbiota, but not arthritis development, in IL-1 receptor antagonist deficient mice – Rebecca Rogier et al. – PLoS One

Microbial metabolite deoxycholic acid shapes microbiota against Campylobacter jejuni chicken colonization – Bilal Alrubaye et al. – PLoS One

Lamb: A novel animal model for regional microbial dysbiosis of the pioneer microbial community – Nilusha Malmuthuge and Philip J. Griebel – Frontiers in Microbiology

** A single bacterium restores the microbiome dysbiosis to protect bones from destruction in a rat model of rheumatoid arthritis – Hudan Pan, Ruijin Guo, Yanmei Ju, Qi Wang et al. – Microbiome

Polybrominated Diphenyl Ethers and Gut Microbiome Modulate Metabolic Syndrome–Related Aqueous Metabolites in Mice – David K. Scoville et al. – Drug Metabolism and Disposition

Animal microbiome

** Incompatible and sterile insect techniques combined eliminate mosquitoes – Xiaoying Zheng et al. – Nature

Commentary: Tiger mosquitoes tackled in a trial – Peter Armbruster – Nature

Host genetics and geography influence microbiome composition in the sponge Ircinia campana – Sarah M. Griffiths et al. – Journal of Animal Ecology

Plant, root and soil microbiome

Non-target Effects of Naphthalene on the Soil Microbial Biomass and Bacterial Communities in the Subalpine Forests of Western China – Liying Lan et al. – Scientific Reports

Drought modulates interactions between arbuscular mycorrhizal fungal diversity and barley genotype diversity – Agnieszka Sendek et al. – Scientific Reports

Variation in rhizosphere microbiota correlates with edaphic factor in an abandoned antimony tailing dump – Enzong Xiao et al. – Environmental Pollution

Structural changes of soil organic matter and the linkage to rhizosphere bacterial communities with biochar amendment in manure fertilized soils – Ruilin Huang & Zhenyi Zhang et al. – Science of the Total Environment

Review: The Postharvest Microbiome: The Other Half of Sustainability – Michael Wisniewski & Samir Droby – Biological Control

Water and extremophile microbiome

Oil degradation potential of microbial communities in water and sediment of Baltic Sea coastal area – Hanna Miettinen et al. – PLoS One

Linking dissolved organic matter composition and bacterioplankton communities in an Amazon floodplain system – Michaela L. de Melo et al. – Limnology and Oceanography

Pollution shapes the bacterial community of a river: a case study – N. Yadav & S. Sharma – International Journal of Environmental Science and Technology

A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments – Jiarui Chen & Shelby E. McIlroy et al. – Microbiome

Phages and viruses

Review: Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut – Tasha M. Santiago-Rodriguez & Emily B. Hollister – Viruses


Targeting 16S rDNA for Stable Recombinant Gene Expression in Pseudomonas – Maike Otto et al. – ACS Synthetic Biology

Microbes in the news

Gut microbes may help malnourished children – Elizabeth Pennisi – Science

The microbiota–gut–brain axis – Natasha Bray – Nature

Nam June Paik Art Center looks at ecosystems, up close – Shim Woo-hyun – The Korea Herald

DuPont Opens State-of-the-Art Probiotics Fermentation Unit – WholeFoods Magazine

The Art Of Solving Antibiotic Overuse in America – ArtIHolics


NIH grant to fund research on microbiome’s role in cancer – Healio

PET TALK: Balanced GI tract plays large role in dog’s overall well-being – Texas A&M University College of Veterinary Medicine & Biomedical Sciences

Mathematics helps us understand the complexity of our microbiome – Tim Sandle – Digital Journal

Good bacteria, bad products – Gali Weinreb – Globes

Gut Microbiome May Alter ALS Progression in Mice – Julianna LeMieux – GenEngNews

Xin’s non-microbiology pick

** The longevity-promoting factor, TCER-1, widely represses stress resistance and innate immunity – Francis R. G. Amrit et al. – Nature Communications

July 3, 2019

Today’s Digest is short with a few articles from Scientific Reports and bioRxiv, spanning six areas, with two highlights added. Enjoy!

General microbiology

Preprint: Single Nanoparticle Tracking Reveals Efficient Long-Distance Undercurrent Transport above Swarming Bacteria – Jingjing Feng et al. – bioRxiv

Human gut microbiome

Preprint (correlation not causation): Parkinson’s disease-associated alterations of the gut microbiome can invoke disease-relevant metabolic changes – Federico Baldini et al. – bioRxiv

Plant, root and soil microbiome

Effect of Straw and Straw Biochar on the Community Structure and Diversity of Ammonia-oxidizing Bacteria and Archaea in Rice-wheat Rotation Ecosystems – Hanlin Zhang et al. – Scientific Reports

Water and extremophile microbiome

Diversity and extracellular enzyme activities of heterotrophic bacteria from sediments of the Central Indian Ocean Basin – Vijayshree S. Gawas et al. – Scientific Reports

Preprint: Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica – Megan Dillon et al. – bioRxiv

** Isolation and characterization of a thermophilic sulfur- and iron-reducing thaumarchaeote from a terrestrial acidic hot spring – Shingo Kato et al. – The ISME Journal

Phages and viruses

** Review: Phage Therapy in the Twenty-First Century: Facing the Decline of The Antibiotic Era; Is it Finally Time for The Age of the Phage? – Shayla Hesse and Sankar Adhya – Annual Review of Microbiology


Preprint: Developing critical thinking in STEM education through inquiry-based writing in the laboratory classroom – Ah Jung Jeon et al. – bioRxiv

Preprint: Genetic research at the intersection of gender identity, sexual orientation, and mental health: community attitudes and recommendations for researchers – Taylor R Thomas et al. – bioRxiv

June 20, 2019

After a week, our Microbiome Digest is back online with a rich collection of articles in all fields microbiome. Highlights include a review on colonization resistance to bacterial pathogens in the gut, a report on daily sampling of the individual microbiome response to similar diets, and, have you heard of the FAIR principles for scientific data? Happy reading!

General microbiology

Bacillus cereus infection in neonates and the absence of evidence for the role of banked human milk: Case reports and literature review – Antoine Lewin et al. – Infection Control & Hospital Epidemiology

Comment: Multiple levels of the unknown in microbiome research – Andrew Maltez Thomas & Nicola Segata – BMC Biology

Comparative genome analysis reveals niche-specific genome expansion in Acinetobacter baumannii strains – Harshita Yakkala & Devyani Samantarrai et al. – PLoS One

Antimicrobial resistance

Definitions and guidelines for research on antibiotic persistence – Nathalie Q. Balaban et al. – Nature Reviews Microbiology

Review: Genomic and metagenomic approaches for predictive surveillance of emerging pathogens and antibiotic resistance – Kimberley V. Sukhum et al. – Clinical Pharmacology & Therapeutics

Review: Antimicrobial Tolerance and Metabolic Adaptations in Microbial Biofilms – Aurélie Crabbé et al. – Trends in Microbiology

Human oral microbiome

Dysbiotic salivary microbiota in dry mouth and primary Sjögren’s syndrome patients – S. Rusthen et al. – PLoS One

Human gut microbiome

** Review: Gut Microbiota and Colonization Resistance against Bacterial Enteric Infection – Q. R. Ducarmon et al. – Microbiology and Molecular Biology Reviews

Review: Gastrointestinal Microbiota in Patients with Chronic Kidney Disease: A Systematic Review – SeonYoon Chung et al. – Advances in Nutrition

Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk – Alexander Kurilshikov et al. – Circulation Research

Commentary: The Microbiome, Plasma Metabolites, Dietary Habits, and Cardiovascular Risk Unravelling Their Interplay – Dariush Mozaffarian – Circulation Research

Review: Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health – Kaitlyn Oliphant & Emma Allen-Vercoe – Microbiome

Review: Lactose digestion in humans: intestinal lactase appears to be constitutive whereas the colonic microbiome is adaptable – Richard A Forsgård – The American Journal of Clinical Nutrition

** Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans – Abigail J. Johnson et al – Cell Host & Microbe

Review: HIV, Cancer, and the Microbiota: Common Pathways Influencing Different Diseases – Sergio Serrano-Villar et al. – Frontiers in Immunology

IDDF2019-ABS-0157 Fecal microbiota transplantations reconstitute gut fungal and viral microbiota in graft-versus-host disease – Fen Zhang et al. – Gut

Exploring the impact of Helicobacter pylori on gut microbiome composition – Nihar Ranjan Dash et al. – PLoS One


Review: Translational Metabolomics: Current Challenges and Future Opportunities – Farhana R. Pinu et al. – Metabolites

Animal experiments

Consumption of post-fermented Jing-Wei Fuzhuan brick tea alleviates liver dysfunction and intestinal microbiota dysbiosis in high fructose diet-fed mice – Xiangnan Zhang et al. – RSC Advance

Mouse: B vitamin sharing promotes stability of gut microbial communities – Vandana Sharma et al. – Frontiers in Microbiology

Variability of the ability of complex microbial communities to exclude microbes carrying antibiotic resistance genes in rabbits – caroline s. achard et al. – Frontiers in Microbiology

Effects of BARLEYmax and high-β-glucan barley line on short-chain fatty acids production and microbiota from the cecum to the distal colon in rats – Seiichiro Aoe et al. – PLoS One

Animal microbiome

The “wildness” of the giant panda gut microbiome and its relevance to effective translocation – Ran Yao & Liangliang Xu et al. – Global Ecology and Conservation

Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle – Fuyong Li et al – Microbiome

Mosquito: Host species and site of collection shape the microbiota of Rift Valley fever vectors in Kenya – David P. Tchouassi et al – PLoS NTD

Longitudinal microbiome profiling reveals impermanence of probiotic bacteria in domestic pigeons – Kirsten Grond, Julie M. Perreau & Wesley T. Loo et al. – PLoS One

Food microbiome

Ground beef microbiome changes with antimicrobial decontamination interventions and product storage – Margaret D. Weinroth et al. – PLoS One

Plant, root and soil microbiome

Biocontrol of Root Diseases and Growth Promotion of the Tuberous Plant Aconitum carmichaelii Induced by Actinomycetes Are Related to Shifts in the Rhizosphere Microbiota – Yulong Li et al. – Microbial Ecology

Microbial communities from different soil types respond differently to organic waste input – Sophie Sadet-Bourgeteau et al. – Applied Soil Ecology

Plant-based oil-sorbents harbor native microbial communities effective in spilled oil-bioremediation under nitrogen starvation and heavy metal-stresses – N. Dashti et al. – Ecotoxicology and Environmental Safety

Effects of agricultural management on rhizosphere microbial structure and function in processing tomato – Jennifer E. Schmidt et al. – Applied and Environmental Microbiology

Microbial diversity in bulk and rhizosphere soil of Ranunculus glacialis along a high-alpine altitudinal gradient – Nadine Praeg et al. – Frontiers in Microbiology

Tripartite Interactions Between Endophytic Fungi, Arbuscular Mycorrhizal Fungi, and Leymus chinensis – Hui Liu et al. – Microbial Ecology

Review: Plant host-associated mechanisms for microbial selection – Piet Jones et al. – Frontiers in Plant Science

Soil Microbial Biomass and Fungi Reduced with Canola Introduced into Long-Term Monoculture Wheat Rotations – Jeremy C. Hansen et al. – Frontiers in Microbiology

Pearls: Microbiota-mediated disease resistance in plants – Nathan Vannier et al. – PLoS Pathogens

Effects of maize rotation on the physicochemical properties and microbial communities of American ginseng cultivated soil – Xiao-Lin Jiao et al. – Scientific Reports

Linking the response of soil microbial community structure in soils to long-term wastewater irrigation and soil depth – Qiuling Dang et al. – Science of the Total Environment

One-time nitrogen fertilization shifts switchgrass soil microbiomes within a context of larger spatial and temporal variation – Huaihai Chen et al. – PLoS One

Water and extremophile microbiome

Comparison of bacterial community structure and potential functions in hypoxic and non-hypoxic zones of the Changjiang Estuary – Dong-Mei Wu & Qiu-Ping Dai et al. – PLoS One

Review: Progress and promise of omics for predicting the impacts of climate change on harmful algal blooms – Gwenn M.M.Hennon & Sonya T.Dyhrman – Harmful Algae

Position-specific metabolic probing and metagenomics of microbial communities reveal conserved central carbon metabolic network activities at high temperatures – Scott C. Thomas et al. – Frontiers in Microbiology

Chemical composition of extracellular polymeric substances and evolution of microbial community in activated sludge exposed to ibuprofen – Guangqing Zhou et al. – Journal of Environmental Management

Enhancement of facultative anaerobic denitrifying communities by oxygen release from roots of the macrophyte in constructed wetlands – Haishu Sun et al. – Journal of Environmental Management

How does environmental inter-annual variability shape aquatic microbial communities? A 40-year annual record of sedimentary DNA from a boreal lake (Nylandssjön, Sweden) – Eric Capo et al. – Frontiers in Ecology and Evolution

Phages and viruses

Review: Virome and bacteriome: two sides of the same coin – Jonathan Stern et al. – Current Opinion in Virology


Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study – Georgina M. Williams et al. – PLoS One

Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination – Josef Dahlberg et al. – PLoS One


GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data – Cuncong Zhong et al. – BMC Bioinformatics

Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets – Annika Brinkmann et al. – Journal of Clinical Microbiology

Microbes in the news

FDA recalls certain tattoo inks for bacterial contamination – Fox 13 News

Viruses found to use intricate ‘treadmill’ to move cargo across bacterial cells – ScienceDaily

USDA issues reminder about how to safely meal prep – Erica Chayes Wida – Today

Highlights and key takeaways from the 2019 Boston Bacterial Meeting (BBM) – Dr. Tomislav Meštrović, MD, Ph.D. – News Medical

Non-microbiology picks

** The State of Open Data Report 2018

Network analysis to evaluate the impact of research funding on research community consolidation – Daniel J. Hicks et al. – PLoS One

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