April 2, 2020

Today’s digest starts with a recent study from The Lancet linking antibiotic usage and the gut microbiome with asthma incidence, before moving onto a range of other papers covering multiple human body sites and environmental microbiome studies.

General microbiome
*** Decreasing antibiotic use, the gut microbiota, and asthma incidence in children: evidence from population-based and prospective cohort studies – Patrick et al. – The Lancet

Human respiratory microbiome

Lung function and microbiota diversity in cystic fibrosis – Cuthbertson et al. – BMC Microbiome

Human gut microbiome

Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease – Ryan et al. – Nature Communications

Fecal microbiota transplantation for the improvement of metabolism in obesity: The FMT-TRIM double-blind placebo-controlled pilot trial – Yu et al. – PLOS Medicine

Effects of underfeeding and oral vancomycin on gut microbiome and nutrient absorption in humans – Basolo et al. – Nature Medicine

The Gut Microbial Diversity of Newly Diagnosed Diabetics but Not of Prediabetics Is Significantly Different from That of Healthy Nondiabetics – Gaike et al. – MSystems

Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation – Rampelli et al. MSystems

Animal experiments

Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice – Tengeler et al. – BMC Microbiome

Unraveling Assemblage, Functions and Stability of the Gut Microbiota of Blattella germanica by Antibiotic Treatment – Domínguez-Santos et al. – Frontiers in Microbiology

Plant, root, and soil microbiome

Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining – Liang et al.  – ISME

Water and extremophile microbiome

Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota – Pan et al. BMC Microbiome

Microbial community profiling of ammonia and nitrite oxidizing bacterial enrichments from brackishwater ecosystems for mitigating nitrogen species – Baskaran et al. – Nature Scientific Reports


Lactobacillus reuteri 5454 and Bifidobacterium animalis ssp. lactis 5764 improve colitis while differentially impacting dendritic cells maturation and antimicrobial responses – Hrdý et al. Nature Scientific Reports

April 1, 2020

Hello Everyone, I am excited for my first post here. Continuing the trend the first few papers are on COVID-19 : first one talks about its classification and nomenclature. I hope everyone is staying safe and healthy. Last but not the least, keep up the hand washing.


* The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2- Coronaviridae Study – Group of the International Committee on Taxonomy of Viruses – Nature Microbiology

Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses – Letko et al. – Nature Microbiology

General microbiome
Variation in prostaglandin metabolism during growth of the diatom Thalassiosira rotula – Dato et al. – Scientific Reports

Pregnancy and early life
Factors affecting early-life intestinal microbiota development – Vandenplas et al. – Nutrition

Multi-site human microbiome
Gut, oral and skin microbiome of Indian patrilineal families reveal perceptible association with age – Chaudhari et al. – Scientific Reports

Human gut microbiome
Implication of the gut microbiome composition of type 2 diabetic patients from northern China – Li et al. – Scientific Reports

The microbiota programs DNA methylation to control intestinal homeostasis and inflammation– Ansari et al. – Nature Microbiology

Animal microbiome
The Contest of Microbial Pigeon Neighbors: Interspecies Competition Between Serratia marcescens and the Human Pathogen Cryptococcus neoformans – Haleva et al. – Fungal Biology

Plant, root, and soil microbiome
Pseudomonas PS01 Isolated from Maize Rhizosphere Alters Root System Architecture and Promotes Plant Growth – Chu et al. – Microorganisms

Phages and viruses
Viruses with different genome types adopt a similar strategy to pack nucleic acids based on positively charged protein domains – Requião et al. – Scientific Reports

*Review: 5 challenges in understanding the role of the virome in health and disease – Wang David – PLOS Pathogens

Whole-genome sequencing of Burkholderia pseudomallei from an urban melioidosis hot spot reveals a fine-scale population structure and localised spatial clustering in the environment – Rachlin et al. – Scientific Reports

Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture – Cummings et al. – Scientific Reports

Review: Potential of proteomics to probe microbes – Matilda et al. – Journal of Basic Microbiology

March 27, 2020

We begin with a few updates about the recent research news about COVID 19 and how as a scientist you might be able to help. As a result of the global lock down, many conferences and seminars have moved online. You will find some of the microbiome-related online events in today’s post. Please also have a look at a special issue of the Philosophical Transactions of the Royal Society for conceptual challenges in microbial community ecology.

Coronavirus vaccines: five key questions as trials begin – Nature News

How blood from coronavirus survivors might save lives – Nature News

COVID-19 Pandemic: Scientist volunteer form

An initiative to redirect scientific resources towards the fight against COVID-19

Virtual Events
Virtual Conference: 6th Annual Translational Microbiome Conference

Guts & Bugs: A virtual GI seminar series by Edelblum Lab

Let’s go viral: online microbiology seminars in partnership with International Society of Microbial Ecology
Schedule can be found via Twitter #MicroSeminar @MicroSeminar

General microbiome
SPECIAL ISSUE: Phillosophical Transactions of the Royal Society B : Conceptual challenges in microbial community ecology

Human respiratory microbiome
Review: Respiratory microbiome and epithelial interactions shape immunity in the lungs – Invernizzi et al. – Immunology

Human oral microbiome
Polymicrobial periodontal disease triggers a wide radius of effect and unique virome – Gao et al. – npj Biofilms and Microbiomes

Metagenomic analysis of bacterial species in tongue microbiome of current and never smokers – Sato et al. – npj Biofilms and Microbiomes

Spatial Ecology of the Human Tongue Dorsum Microbiome – Wilbert et al. – Cell Reports

Oral biofilms exposure to chlorhexidine results in altered microbial composition and metabolic profile – Chatzigiannidou et al. – npj Biofilms and Microbiomes

Dysbiotic oral microbiota and infected salivary glands in Sjögren’s syndrome – Alam et al. – PLOS ONE

Animal experiments
Drosophila-associated bacteria differentially shape the nutritional requirements of their host during juvenile growth – Consuegra et al. – PLOS Biology

Bacterially produced metabolites protect C. elegans neurons from degeneration – Urrutia et al. – PLOS Biology

Dynamic interactions within the host-associated microbiota cause tumor formation in the basal metazoan Hydra – Rathje et al. – PLOS Pathogens

Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice – Jangid et al. – PLOS ONE

Variations in microbiota composition of laboratory mice influence Citrobacter rodentium infection via variable short-chain fatty acid production – Osbelt et al. – PLOS Pathogens

Changes in the faecal microbiota of horses and ponies during a two-year body weight gain programme – Langner et al. – PLOS ONE

Animal microbiome
Microbiomes in the insectivorous bat species Mops condylurus rapidly converge in captivity – Edenborough et al. – PLOS ONE

Plant, root, and soil microbiome
Towards Nutrition-Sensitive Agriculture: An evaluation of biocontrol effects, nutritional value, and ecological impact of bacterial inoculants – Passera et al. – Science of The Total Environment

Book Chapter: Rhizobacteria Versus Chelating Agents: Tool for Phytoremediation – Kaur et al. – Microbial Technology for Health and Environment

Book Chapter: Applications of Microorganisms in Agriculture – Doley et al. – Microbial Technology for Health and Environment

Plant Invasion Has Limited Impact on Soil Microbial alpha Diversity: A Meta-Analysis – Custer & van Diepen – Diversity

Water microbiome
Carbonate facies‐specific stable isotope data record climate, hydrology, and microbial communities in Great Salt Lake, UT – Ingalls et al. – Geobiology

The microbiome of modern microbialites in Bacalar Lagoon, Mexico – Yanez-Montalvo et al. – PLOS ONE

Food microbiology
Variations in Fungal Community and Diversity in Doushen With Different Flavors – Luo et at. – Frontiers in Microbiology

MetaBridge: An Integrative Multi‐Omics Tool for Metabolite‐Enzyme Mapping – Blimkie et al. – Current Protocols in Bioinformatics

Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: A case study using coastal marine eDNA – McClenaghan et al. – PLOS ONE

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph – Gautreau et al. – PLOS Computational Biology

The Community Simulator: A Python package for microbial ecology – Marsland et al. – PLOS ONE

Genome-based species-specific primers for rapid identification of six species of Lactobacillus acidophilusgroup using multiplex PCR – You & Kim – PLOS ONE

Pathogens and microbiome
Commensal Neisseria cinerea impairs Neisseria meningitidis microcolony development and reduces pathogen colonisation of epithelial cells – Custodio et al. – PLOS Pathogens

Swimming motility of a gut bacterial symbiont promotes resistance to intestinal expulsion and enhances inflammation – Wiles et al. – PLOS Biology

March 26th, 2020

This is my first post on the site! There weren’t a lot of alerts today, so I dug around for other papers I can find. Today’s digest includes mostly human microbiome research, most notably a study identifying a staph peptide that induces acute exacerbation of pulmonary fibrosis, as well as a very diverse epidemiological study of the impact of diet on the gut microbiome in the United States.

General Human Microbiome

US nativity and dietary acculturation impact the gut microbiome in a diverse US population  – Peters, B.A., Yi, S.S., Beasley, J.M. et al. – ISME

Microbiome in Pregnancy and Birth

Maternal carriage of Prevotella during pregnancy associates with protection against food allergy in the offspring – Vuillermin, P.J., O’Hely, M., Collier, F. et al. – Nature Communications

Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species – Mehta, O., Ghosh, T.S., Kothidar, A. et al. – Microbial Ecology

Translational human microbiome research

A Staphylococcus pro-apoptotic peptide induces acute exacerbation of pulmonary fibrosis – D’Alessandro-Gabazza, C.N., Kobayashi, T., Yasuma, T. et al. – Nature Communications

Effect of probiotics during vonoprazan‐containing triple therapy on gut microbiota in Helicobacter pylori infection: A randomized controlled trial – Kakiuchi et al. – Helicobacter

Rosuvastatin alters the genetic composition of the human gut microbiome – Kummen, M., Solberg, O.G., Storm-Larsen, C. et al. – Scientific Reports

Microbiome and Cancer

Metaproteomics characterizes human gut microbiome function in colorectal cancer – Long, S., Yang, Y., Shen, C. et al. – npj Biofilms and Microbiomes

Plant microbiome

Genome‐resolved metagenomics to study co‐occurrence patterns and intraspecific heterogeneity among plant pathogen metapopulations – Newberry et al. – Environmental Microbiology

Symbiotic nitrogen fixation and endophytic bacterial community structure in Bt-transgenic chickpea (Cicer arietinum L) – Alok, D., Annapragada, H., Singh, S. et al. – Scientific Reports

Soil microbiome

Soil Microbial Diversity Affects the Plant-Root Colonization by Arbuscular Mycorrhizal Fungi – Ferreira et al. – Microbial Ecology

Bioinformatics/Sequencing analysis methods

Joining Illumina paired-end reads for classifying phylogenetic marker sequences – Liu et al. – BMC Bioinformatics

M2IA: a Web Server for Microbiome and Metabolome Integrative Analysis – Ni et al. – Bioinformatics


Alcohol pretreatment of stools effect on culturomics – Afouda, P., Hocquart, M., Pham, T. et al. – Scientific Reports

Pre-prints on bioRxiv to look forward to

Infant gut microbiome

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics – West et al. (Side note: The Banfield lab produces a lot of good work!)

Laboratory work on bacterial motility in the gut

Bacterial Swarmers exhibit a Protective Response to Intestinal Stress – Chen et al.

Long-read sequencing of gut mycobiome

Assessing anaerobic gut fungal (Neocalliamstigomycota) diversity using PacBio D1/D2 LSU rRNA amplicon sequencing and multi-year isolation – Hanafy et al.


HumGut: A comprehensive Human Gut prokaryotic genomes collection filtered by metagenome data


March 25, 2020

Today’s digest features an article about colorectal cancer signatures and E. coli and a study about the microbiome and resistome of great apes and human.


News: How blood from coronavirus survivors might save lives – Nature

General microbiome

What is the Origin of Human Bacterial Flora? – Alen J Salerian – Journal of Applied & Environmental Microbiology

The Microbiome of the Nose—Friend or Foe? – Sofia Dimitri-Pinheiro – Allergy Rhinol.

Pregnancy and early life

Non-targeted urinary metabolomics in pregnancy and associations with fetal growth restriction – Chelsea M. Clinton – Scientific Reports

Multi-site human microbiome

Effects of Chlorhexidine mouthwash on the oral microbiome – Raul Bescos – Scientific Reports

Human gut microbiome

Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli – Cayetano Pleguezuelos-Manzano – Nature

Animal experiments

Natural agents inhibit colon cancer cell proliferation and alter microbial diversity in mice – Lulu Farhana – PLOS One

Animal microbiome (for animals in the wild)

Co-abundance analysis reveals hidden players associated with high methane yield phenotype in sheep rumen microbiome – Leila Ghanbari Maman – Scientific Reports

Effects of heat stress on the gut health of poultry – Marcos H Rostagno – Journal of Animal Science

The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography – Tayte P. Campbell – THE ISME Journal

Plant, root, and soil microbiome

Impact of molasses and microbial inoculants on fermentation quality, aerobic stability, and bacterial and fungal microbiomes of barley silage – Beiyi Liu – Scientific Reports

Bacterial analysis in the early developmental stages of the black tiger shrimp (Penaeus monodon) – Pacharaporn Angthong – Scientific Reports

Water and extremophile microbiome

Microbial community profiling of ammonia and nitrite oxidizing bacterial enrichments from brackishwater ecosystems for mitigating nitrogen species – Viswanathan Baskaran – Scientific Reports

Vertical Beta-Diversity of Bacterial Communities Depending on Water Stratification – Wan-Hsuan Cheng – Frontiers in Microbiology


Artificial microbiome heterogeneity spurs six practical action themes and examples to increase study power-driven reproducibility – Abigail R. Basson – Scientific Reports


Benchmarking the MinION: Evaluating long reads for microbial profiling – Robert M. Leidenfrost – Scientific Reports

March 20, 2020

Good morning! I hope this post finds you well. There are lots of new microbiome papers to share, including work on the disruption of E. coli biofilms, inconsistent diets used in Drosophila microbiome studies, and the effects of pollution on soil microbial communities.

General microbiome

Biosynthesis of silver nanoparticles by Fusarium scirpi and its potential as antimicrobial agent against uropathogenic Escherichia coli biofilms, Candelario Rodríguez-Serrano et al., PLOS ONE

Human gut microbiome

Targeted inhibition of gut bacterial β-glucuronidase activity enhances anticancer drug efficacy, Aadra P. Bhatt et al., PNAS

Gut Microbiome Pattern Reflects Healthy Aging and Predicts Extended Survival in Humans (preprint), Tomasz Wilmanski et al., bioRxiv

Propionic Acid Shapes the Multiple Sclerosis Disease Course by an Immunomodulatory Mechanism, Alexander Duscha et al., Cell

Adjusting for age improves identification of gut microbiome alterations in multiple diseases, Tarini S Ghosh et al., eLife

Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms, Jian Sun et al., Nature Communications

Review – Altering Routine Intensive Care Unit Practices to Support Commensalism, Hamilton and Behal, Nutrition in Clinical Practice

Household Pet Ownership and the Microbial Diversity of the Human Gut Microbiota, Ashley E. Kates et al., Frontiers in Cellular and Infection Microbiology

Meta-analysis – Assessing the efficacy and safety of fecal microbiota transplantation and probiotic VSL#3 for active ulcerative colitis: A systematic review and meta-analysis, Xiaofei Dang et al., PLOS ONE

Other human microbiome

Subgingival Host-Microbial Interactions in Hyperglycemic Individuals, P.S. Kumar et al., Journal of Dental Research

Investigating Bifidobacteria and Human Milk Oligosaccharide Composition of Lactating Mothers, Gabriele Andrea Lugli et al., FEMS Microbiology Ecology

Animal experiments

Effects of intestinal flora on the pharmacokinetics and pharmacodynamics of aspirin in high-altitude hypoxia, Sun and Zhang et al., PLOS ONE

Meta-analysis of diets used in Drosophila microbiome research and introduction of the Drosophila Dietary Composition Calculator (DDCC) (preprint), Broderick and Lesperance, bioRxiv

The Carnivorous Digestive System and Bamboo Diet of Giant Pandas May Shape Their Low Gut Bacterial Diversity, Wei Gui et al., Conservation Physiology

Animal microbiome

Non-invasive evaluation of the equine gastrointestinal mucosal transcriptome, Coleman and Whitfield-Cargile et al., PLOS ONE

Dietary substitution of soybean oil with coconut oil in the absence of dietary antibiotics supports growth performance and immune function in nursery and grower pigs, Andrea G. Braundmeier-Fleming et al., Journal of Animal Science and Biotechnology

Isoflavone supplementation, via red clover hay, alters the rumen microbial community and promotes weight gain of steers grazing mixed grass pastures, Brittany E. Harlow et al., PLOS ONE

Domesticated equine species and their derived hybrids differ in their fecal microbiota, J.E. Edwards et al., Animal Microbiome

Integrative analysis of gut microbiome and metabolites revealed novel mechanisms of intestinal Salmonella carriage in chicken, Khin K.Z. Mon et al., Scientific Reports

Plant, root, and soil microbiome

Acute effects of PAH contamination on microbial community of different forest soils, Enrica Picariello et al., Environmental Pollution

Context-dependent Dynamics Lead to the Assembly of Functionally Distinct Microbial Communities, Leonora S Bittleston et al., Nature Communications

Lifting the veil on arid-to-hyperarid Antarctic soil microbiomes: a tale of two oases, Eden Zhang et al., Microbiome

Perspective – Toward Comprehensive Plant Microbiome Research, Kari Saikkonen et al., Frontiers in Ecology and Evolution

Water and extremophile microbiome

Deep-sea corals provide new insight into the ecology, evolution, and the role of plastids in widespread apicomplexan symbionts of anthozoans, Samuel A. Vohsen et al., Microbiome

Food microbiology

Lactic Acid Bacteria Isolated From Korean Kimchi Activate the Vitamin D Receptor–autophagy Signaling Pathways, Rong Lu et al., Inflammatory Bowel Diseases

Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome, Bryn C. Taylor et al., mSystems

Differential Microbial Composition of Monovarietal and Blended Extra Virgin Olive Oils Determines Oil Quality During Storage, Zullo and Ciafardini, Microorganisms

Phages and viruses

Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota, Germán Bonilla-Rosso et al., PNAS


FORENSIC: an Online Platform for Fecal Source Identification, Adélaïde Roguet et al., mSystems

Review – Accurate and complete genomes from metagenomes, Lin-Xing Chen et al., Genome Research

Powmic: An R Package for Power Assessment in Microbiome Case-Control Studies, Li Chen, Bioinformatics


RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs, Leyuan Li et al., Microbiome

Non-microbiology picks

Marketplace shrimp mislabeling in North Carolina, Morgan L. Korzik et al., PLOS ONE

March 16, 2020

To all the work-from-home researchers (like me!), today’s digest covers microbiome in memory recognition, enteric neuropathy and neurodevelopmental disorder in rodent models. Gut microbiome in cardiovascular disease, a dual mechanism antibiotic and shifts in human gut microbiome and metabolome following gastric bypass. An important preprint that Covid-19 could not induce reinfection in infected rhesus macaques and that Ibuprofen may aggravate Covid-19 infection.

General microbiome

Gut microbiota and cardiovascular disease: opportunities and challenges – Negin Kazemian – Microbiome

Human microbiome
Pharmacomicrobiomics in inflammatory arthritis: gut microbiome as modulator of therapeutic response – Jose U. Scher – Nature Reviews Rheumatology

Long-term metal exposure changes gut microbiota of residents surrounding a mining and smelting area – Mengmeng Shao – Scientific Reports

Temporospatial shifts in the human gut microbiome and metabolome after gastric bypass surgery – Zehra Esra Ilhan – NPJ biofilms and microbiomes

Animal experiments

Habitat and seasonality shape the structure of tench (Tinca tinca L.) gut microbiome – Tomasz Dulski – Scientific Reports

Microecological Koch’s postulates reveal that intestinal microbiota dysbiosis contributes to shrimp white feces syndrome – Zhijian Huang – Microbiome

Early-life microbial intervention reduces colitis risk promoted by antibiotic-induced gut dysbiosis – Jun Miyoshi – BioRxiv

Gut microbiota manipulation during the prepubertal period shapes behavioral abnormalities in a mouse neurodevelopmental disorder model – Justin M. Saunders – Scientific Reports

Minocycline-induced microbiome alterations predict cafeteria diet-induced spatial recognition memory impairments in rats – Sarah-Jane Leigh – Translational Psychiatry

A purified membrane protein from Akkermansia muciniphila or the pasteurised bacterium blunts colitis associated tumourigenesis by modulation of CD8+ T cells in mice – Lijuan Wang – Gut

PM2.5 exposure perturbs lung microbiome and its metabolic profile in mice – Jingli Li – Science of The Total Environment

High‐fat diet–induced alterations to gut microbiota and gut‐derived lipoteichoic acid contributes to the development of enteric neuropathy – Yvonne Nyavor – Neurogastroenterology and Motility

Plant, root and soil microbiome

Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil – L. V. Alteio – mSystems

Impact of plants on the diversity and activity of methylotrophs in soil – Michael C. Macey – Microbiome

Conserved bacterial genomes from two geographically distinct peritidal stromatolite formations shed light on potential functional guilds – Samantha C. Waterworth – BioRxiv


A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures – Nathan D. Olson – Microbiome

Antibiotic resistance

A dual-mechanism antibiotic targets Gram-negative bacteria and avoids drug resistance – James K. Martin – BioRxiv

Non microbiology picks

Reinfection could not occur in SARS-CoV-2 infected rhesus macaques – Linlin Bao – BioRxiv

Anti-inflammatories may aggravate Covid-19, France advises – The Guardian