April 26, 2020

Greetings from Pittsburgh, PA!

Today’s digest includes several reviews, numerous host-microbiome studies, a wide variety of environmental microbiome studies, and a new book focused on Emerging Technologies in Environmental Bioremediation.

I also wanted to highlight the virtual Fermentation Mini-Seminars offered by the Applied Ecology Department at my alma mater, NC State University. During the first seminar of the series I learned about the Wild Sourdough Project, which is a community-science/citizen-science project where participants can submit observational data about their sourdough culture. If you’re missing the lab, this might be the perfect project for you!

Virtual Events

NCSU Fermentation Mini-Seminars offered every Thursday at 4pm EST from April through August

General microbiome

Special Issue: Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals – De Vrieze et al. – Microbial Biotechnology

Review: Biofilm matrixome: Extracellular components in structured microbial communities – Karygianni et al. – Trends in Microbiology

Review: Microbial symbiosis: A network towards biomethanation – Saha et al. – Trends in Microbiology

Multi-site human microbiome

Microbiota in cerebrovascular disease: A key player and future therapeutic target – Tonomura et al. – Journal of Cerebral Blood Flow & Metabolism

Review: Role of microbiome and antibiotics in autoimmune diseases – Vangoitsenhoven and Cresci – Nutrition in Clinical Practice

Human skin microbiome

Isolation and characterization of diverse microbial representatives from the human skin microbiome – Timm et al. – BMC Microbiology

Human gut microbiome

Altered gut microbial profile is associated with abnormal metabolism activity of Autism Spectrum Disorder – Dan et al. – Gut Microbes

Seasonal variation in gut microbiota composition: cross-sectional evidence from Ukrainian population – Koliada et al. – BMC Microbiology

Gut microbiome reveals specific dysbiosis in primary osteoporosis – Xu et al. – Frontiers in Cellular and Infection Microbiology

Animal experiments

The clinical drug Ebselen attenuates inflammation and promotes microbiome recovery in mice after antibiotic treatment for CDI – Garland et al. – Cell Reports Medicine

Effect of oxytetracycline treatment on the gastrointestinal microbiome of critically endangered white abalone (Haliotis sorenseni) treated for withering syndrome – Parker-Graham et al. – Aquaculture

Effects of hydrolyzed fish protein and autolyzed yeast as substitutes of fishmeal in the gilthead sea bream (Sparus aurata) diet, on fish intestinal microbiome – Rimoldi et al. – BMC Veterinary Research

Animal microbiome

(My microbiome) would walk 10,000 miles: Maintenance and turnover of microbial communities in introduced dung beetles – Parker et al. – Invertebrate Microbiology

Plant, root, and soil microbiome

Nocardiopsis deserti sp. nov., isolated from a high altitude Atacama Desert soil – Asem et al. – International Journal of Systemic and Evolutionary Microbiology

Steel slag amendment impacts on soil microbial communities and activities of rice (Oryza sativa L.) – Das et al. – Scientific Reports

Peat properties, dominant vegetation type and microbial community structure in a tropical peatland – Girkin et al. – Wetlands

Integrating transcriptomics and metabolomics to studies key metabolism, pathways and candidate genes associated with drought-tolerance in Carthamus tinctorius L. under drought stress – Wei et al. – Industrial Crops and Products

Dynamics of ammonia oxidizers and denitrifiers in response to compost addition in black soil, Northeast China – Yang et al. – PeerJ

Water and extremophile microbiome

Impacts of an eruption on cold-seep microbial and faunal dynamics at a mud volcano – Girard et al. – Frontiers in Marine Science

Unraveling heterogeneity of coral microbiome assemblages in tropical and subtropical corals in the South China Sea – Gong et al. – Microorganisms

Anode potential-dependent protection of electroactive biofilms against metal ion shock via regulating extracellular polymeric substances – Hou et al. – Water Research

Microbial ecology and biogeochemistry of hypersaline sediments in Orca Basin – Nigro et al. – PLOS One

Near streambed flow shapes microbial guilds within and across trophic levels in fluvial biofilms – Risse-Buhl et al. – Limnology and Oceanography

Heterotrophic sulfide-oxidizing nitrate-reducing bacteria enables the high performance of integrated autotrophic-heterotrophic denitrification (IAHD) process under high sulfide loading – Zhang et al. – Water Research

Built environment (subways, indoor surfaces)

Ecological processes affecting long-term eukaryote and prokaryote biofilm persistence in nitrogen removal from sewage – Angell et al. – Genes

Long-term microbial community dynamics in a pilot-scale gas sparged anaerobic membrane bioreactor treating municipal wastewater under seasonal variations – Kannan et al. – Bioresource Technology

Book: Emerging Technologies in Environmental Bioremediation – Edited by Shah et al.

Food microbiology

How processing methods affect the microbial community composition in a cereal-based fermented beverage – Phiri et al. – LWT – Food Science and Technology

High-throughput sequencing and metabolomics reveal differences in bacterial diversity and metabolites between red and white sufu – Tang et al. – Frontiers in Microbiology

April 19, 2020

Hello from the Sonoran Desert! It is a lovely morning here in Tucson, Az. I am excited to send my first contribution to Microbiome Digest! There is a lot of diversity in today’s digest, but if microbes thriving in all kinds of strange, extreme conditions are your area of interest, you’ll be interested in the book compiling the latest studies on extremophiles. Each chapter focuses on a particular environment, ranging from deserts to deep-sea hydrothermal vents, and explores the mechanisms allowing microbes to survive these incredible conditions.

If like me, you are a computational biology enthusiast and a machine learning addict, you should enjoy reading the last entry, a short perspective paper examining how machine learning algorithms can help predict antibiotic resistance!

Have a great Sunday!

General microbiology

Preprint: Interspecies interactions in bacterial colonies are determined by physiological traits and the environment – Booth – BioRxiv

Human gut and mouth microbiome

Bacterial colonization reprograms the neonatal gut metabolome – Bittinger – Nature microbiology

Salivary Factors that Maintain the Normal Oral Commensal Microflora – Carpenter – Journal of dental research

Preprint: Metagenomic Next-Generation Sequencing of Rectal Swabs for the Surveillance of Antimicrobial Resistant Organisms on the Illumina Miseq and Oxford MinION Platforms – Yee – bioRxiv

Animal microbiome

Preprint: Mortality of native and invasive ladybirds co-infected by ectoparasitic and entomopathogenic fungi – Haelewaters – bioRxiv

Built environment

Preprint: The Microbes Found in the Honey of New York City Beehives – Weiss – BioRxiv

Correlation between autochthonous microbial communities and key odorants during the fermentation of red pepper (Capsicum annuum L.) – Xu – Food Microbiology

Water and extremophile microbiome

Book: Microbial Versatility in Varied Environments: Microbes in Sensitive Environments – collective – Springer Nature

The seasonal variation of microbial communities in drinking water sources in Shanghai – Guo – Journal of Cleaner Production

Plant, root and soil microbiome

LDPE microplastics significantly alter the temporal turnover of soil microbial communities –  Wang – Science of the total environment

High abundance of Ralstonia solanacearum changed tomato rhizosphere microbiome and metabolome – Wen – BMC Plant Biology

Phages and viruses

Preprint : First evidence of virus-like particles in the bacterial symbionts of Bryozoa – Vishnyakov – BioRxiv

Microbial community development on model particles in the deep sulfidic waters of the Black Sea – Suominen – Environmental microbiology

The stepwise assembly of the neonatal virome is modulated by breastfeeding – Liang – Nature


Preprint: Bayesian classification, anomaly detection, and survival analysis using network inputs with application to the microbiome – Josephs – arXiv


Preprint: Expanding the diversity of bacterioplankton isolates and modeling isolation efficacy with large scale dilution-to-extinction cultivation – Henson – bioRxiv

Catalyzing rapid discovery of gold-precipitating bacterial lineages with university students – Riley – PeerJ

COVID-19 and career

Science-ing from home – Powell – Nature

My non-microbiology pick

Perspective: Lean, mean, learning machines – Wheeler – Nature review microbiology

April 16, 2020

Greetings from Pittsburgh, PA! I’ve been following Microbiome Digest for several years, but this is my first contribution. Although my research is in a different subject area now, my PhD work focused on host-associated microbiota. That topic still has a special place in my heart, so below you’ll find research articles focused on the microbiota of calves, honey bees, dogs, giant clams, mosquitos, and bats! If host-associated microbiota isn’t your topic of interest, I’ve also included other articles so you can learn “WhatsGNU” in microbiology!

General microbiome

Review: A benchmark of algorithms for the analysis of pooled CRISPR screens – Bodapati et al. – Genome Biology

Animal experiments

Comparison of the ruminal and fecal microbiotas in beef calves supplemented or not with concentrate – Lourenco et al. – PLOS One

The trisaccharide melezitose impacts honey bees and their intestinal microbiota – Seeburger – PLOS One

Fecal shedding of Salmonella spp., Clostridium perfringens, and Clostridioides difficile in dogs fed raw meat-based diets in Brazil and their owners’ motivation – Viegas et al. – PLOS One

Mechanistic molecular responses of the giant clam Tridacna crocea to Vibrio coralliilyticus challenge – Xu et al. – PLOS One

Animal microbiome

Metagenomic analysis of Aedes aegypti and Culex quinquefasciatus mosquitoes from Grenada, West Indies – Ramos-Nino et al. – PLOS One

Detection of novel coronaviruses in bats in Myanmar – Valitutto et al. – PLOS One

Plant, root, and soil microbiome

Plant microbiome analysis after Metarhizium amendment reveals increases in abundance of plant growth-promoting organisms and maintenance of disease-suppressive soil – Barelli et al. – PLOS One

The genome evolution and domestication of tropical fruit mango – Wang et al. – Genome Biology

Water and extremophile microbiome

Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica – Dillion et al. – PLOS One

Preprint: Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy – Metcalfe et al. – bioRxiv

Built environment

A comparative analysis of drinking water employing metagenomics -Brumfield et al. – PLOS One

Prevalence and pollution characteristics of antibiotic resistant genes in one high anthropogenically-impacted river – Li and Zhang – PLOS One

Longitudinal survey of microbiome associated with particulate matter in a megacity – Qin et al. – Genome Biology

Phages and viruses

Ozone efficacy for the control of airborne viruses: Bacteriophage and norovirus models – Dubuis et al. – PLOS One


Decode-seq: a practical approach to improve differential gene expression analysis – Li et al. – Genome Biology

WhatsGNU: a tool for identifying proteomic novelty – Moustafa and Planet – Genome Biology

A Zipf-plot based normalization method for high-throughput RNA-seq data – Wang – PLOS One

April 11, 2020

Happy Saturday morning, y’all! I’m excited for my first contribution to the digest, and hope you enjoy my picks over a luxurious weekend meal. Today’s digest starts with some preprints about COVID including research on a drug that may inhibit viral replication. Other research highlights include an examination of the relationship between the vaginal microbiome and pre-term birth, a preprint on the oral microbiome in space, and a potential new technique for low cost, high-throughput metagenome profiling. Scroll all the way to the end for information about a fun project by a University of Wyoming student called The Microbestiary.

Preprint: Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses. Auslander, N. et al.

Preprint: Nelfinavir inhibits replication of severe acute respiratory syndrome coronavirus 2 in vitro. Yamamoto, N. et al.

Preprint: Understanding the B and T cells epitopes of spike protein of severe respiratory syndrome coronavirus-2: A computational way to predict the immunogens. Vashi, Y. et al.

General Microbiome
Preprint: From iron to antibiotics: Identification of conserved bacterial-fungal interactions across diverse partners. Pierce, EC. et al.

Human Gut Microbiome
Review: Unraveling Host-Gut Microbiota Dialogue and Its Impact on Cholesterol Levels. Villette R. et al. Frontiers in Pharmacology.

Metagenomics analysis reveals features unique to Indian distal gut microbiota. Kaur, K. et al. PLOS ONE.

Gut Microbiota Modulate CD8 T Cell Responses to Influence Colitis-Associated Tumorigenesis. Yu, A.I. et al. Cell Reports.

Human Oral Microbiome
Preprint: Characterization of the oral microbiome of medically controlled type-2 diabetes patients. Santos, A. et al.

Human Vaginal Microbiome
Cervicovaginal microbiome and natural history of HPV in a longitudinal study. Usyk, M. et al. PLOS Pathogens.

Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth. Kosti, I. et al. Frontiers in Microbiology.

Water and Extremophile Microbiome
Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef. Hartman, L.M. et al. Animal Microbiome.

Microbial Diversity and Metabolic Potential in the Stratified Sansha Yongle Blue Hole in the South China Sea. He, P. et al. Scientific Reports.

Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources. Compte-Port, S. et al. PLOS ONE.

Animal Experiments and Animal Microbiome
The skin microbiome facilitates adaptive tetrodotoxin production in poisonous newts. Vaelli, P.M. et al. eLife.

Metatranscriptomic virome assessment of Rhipicephalus microplus from Colombia. Gomez, G.F. et al. Ticks and Tick-borne Diseases.

Preprint: Metabolic differences between symbiont subpopulations in the deep-sea tubeworm Riftia pachyptila. Hinzke, T. et al.

Preprint: Similar gut bacterial microbiota in two fruit-feeding moth pests collected from different host species and locations. Gong, Q et al.

Plant, Root, and Soil Microbiome
The preceding root system drives the composition and function of the rhizosphere microbiome. Zhou, Y. et al. Genome Biology.

Microbial Co-Occurrence in Floral Nectar Affects Metabolites and Attractiveness to a Generalist Pollinator. Rering, C.C. et al. Journal of Chemical Ecology.

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios. Braga, L.P.P. et al. Microbiome.

A predatory myxobacterium controls cucumber Fusarium wilt by regulating the soil microbial community. Ye, X. et al. Microbiome.

A plant genetic network for preventing dysbiosis in the phyllosphere. Chen, T. et al. Nature.

Fungal communities differentially respond to warming and drought in tropical grassland soil. de Oliveira, T.B. et al. Molecular Ecology.

Built Environment
An in-depth survey of the microbial landscape of the walls of a neonatal operating room. Derilus, D. et al. PLOS ONE.

Microbes in Space
Preprint: Defining the resilience of the human salivary microbiota by a 520 days longitudinal study in confined environment: the Mars500 mission. Bacci, G. et al.

Phages and Viruses
Phage cocktail containing Podoviridae and Myoviridae bacteriophages inhibits the growth of Pectobacterium spp. under in vitro and in vivo conditions. Zaczek-Moczydłowska, M.A. et al. PLOS ONE.

Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses. Moniruzzaman M., et al. Nature Communications.

Preprint: Infection with novel Bacteroides phage BV01 alters host transcriptome and bile acid metabolism in a common human gut microbe. Campbell, D.E. et al.

Preprint: Integrative and Conjugative Elements (ICE) and Associated Cargo Genes within and across Hundreds of Bacterial Genera. Kaufman, J. et al.

A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling. Hess, M.K. et al. PLOS ONE.

Industrial Microbiome
Open microbiome dominated by Clostridium and Eubacterium converts methanol into i-butyrate and n-butyrate. Huang, S. et al. Applied Microbiology and Biotechnology.

Fun with Microbes
University of Wyoming masters student Erin Bentley was selected for an Arctic Circle Expedition in 2021 where she will characterize microbes and share her discoveries on The Microbestiary.
“The Microbestiary strives to show the public, in welcoming and memorable ways, that the microbial world is populated by strange and beautiful characters,” says Bentley in an article published on the UW website.

April 7, 2020

Hi everyone! This is my first contribution to the daily digest, and I’ll follow others’ lead by starting with the latest preprints concerning Covid-19. Away from the ongoing pandemic, some of the highlights include a look at how commensal gut microbes interact with pathogens, and an insight into deep sea oceanic crust microbiomes.

It seems to be a relatively quiet day today, so I’ve included an article from the University of Bristol which looks at how nanoscopic pillars on the surface of some insect wings protect them against bacteria. Perhaps only loosely a microbiome paper, but it’s worth a read for its electron microscopy alone!


Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor – Lan et al. – Nature

Preprint: Atazanavir inhibits SARS-CoV-2 replication and pro-inflammatory cytokine production – Fintelman-Rodrigues et al.

Preprint: Amantadine disrupts lysosomal gene expression; potential therapy for COVID19 – Smieszek et al.

Preprint: Potent Antiviral Activities of Type I Interferons to SARS-CoV-2 Infection – Mantlo et al.

Human gut microbiome

Dissecting individual pathogen-commensal interactions within a complex gut microbiota community – Hassall and Unnikrishnan

Animal microbiome

Antibacterial effects of nanopillar surfaces are mediated by cell impedance, penetration and induction of oxidative stress – Jenkins et al. – Nature Communications

Water and extremophile microbiome

Deep microbial proliferation at the basalt interface in 33.5–104 million-year-old oceanic crust – Suzuki et al.Communications Biology

Food microbiology

How does the microbiome impact pig health? – Sarah Mikesell – The Pig Site

Microbes in the news

Lifestyle trumps geography in determining makeup of gut microbiomeEurekAlert!

Microbes on the market

Gilead taps Second Genome for microbiome biomarker help in a potential $1.5B deal – Connor Hale – FierceBiotech.com

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

March 5, 2020

Today’s Digest is heavy, so you might want to pace yourself. It’s hard to pick the highlights, but I’m biased towards fungal research, so first about a wake-up call to look at the fungi seriously. The insects might provide for remedy against antibiotic resistance and is the dust settled on the sparse fetal intestinal microbiota? Stay healthy and keep reading.


Call for papers – Global Outbreaks and Responses – BMC Medicine

General microbiology

** Viewpoints: Fungal diseases as neglected pathogens: A wake-up call to public health officials – Marcio L. Rodrigues & Joshua D. Nosanchuk – PLoS NTD

Inducible cell-to-cell signaling for tunable dynamics in microbial communities – Arianna Miano et al. – Nature Communications

Antimicrobial resistance

** The insect antimicrobial peptide cecropin A disrupts uropathogenic Escherichia coli biofilms – Miriam Kalsy et al. – npj Biofilms and Microbiomes

Using comparative genomics to understand molecular features of carbapenem-resistant Acinetobacter baumannii from South Korea causing invasive infections and their clinical implications – Min Hyung Kim – PLoS One

Factors associated with sufficient knowledge of antibiotics and antimicrobial resistance in the Japanese general population – Shinya Tsuzuki et al. – Scientific Reports

Faeces and vaccines could be the key to tackling antimicrobial resistance – Elisabeth Mahase – BMJ

A survey of extended-spectrum beta-lactamase-producing Enterobacteriaceae in urban wetlands in southwestern Nigeria as a step towards generating prevalence maps of antimicrobial resistance – Olawale Olufemi Adelowo et al. – PLoS One

Pregnancy and early life

** Viable bacterial colonization is highly limited in the human intestine in utero – E. Rackaityte et al. – Nature Medicine

Perinatal Antibiotic Exposure Affects the Transmission between Maternal and Neonatal Microbiota and Is Associated with Early-Onset Sepsis – Ping Zhou et al. – mSphere

Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut – Yonatan Sher et al. – PLoS One

Human skin microbiome

A microbiome and metabolomic signature of phases of cutaneous healing identified by profiling sequential acute wounds of human skin: An exploratory study – Mohammed Ashrafi et al. – PLoS One

Human oral microbiome

Review: Single-Cell Genomics and the Oral Microbiome – M. Balachandran et al. – Journal of Dental Research

Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts – B. Bor et al. – Journal of Dental Research

Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection – Smruti Pushalkar et al. – iScience

Press: Oral Microbiome Changes Implicated in Gum Inflammation in E-Cigarette Users – GenomeWeb

In vitro: A salivary metabolite signature that reflects gingival host-microbe interactions: instability predicts gingivitis susceptibility – Marcela M. Fernandez-Gutierrez et al. – Scientific Reports

Human respiratory microbiome

Review: The Role of Lung and Gut Microbiota in the Pathology of Asthma – Weronika Barcik et al. – Immunity

Cancer and microbiome

Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth – Elena Zagato et al. – Nature Microbiology

Escherichia coli adhesion portion FimH functions as an adjuvant for cancer immunotherapy – Wei Zhang et al. – Nature Communications

Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy – Ling Ling Chua et al. – BMC Cancer

Review: Interplay between Dietary Polyphenols and Oral and Gut Microbiota in the Development of Colorectal Cancer – Carolina Cueva & Mariana Silva – Nutrients

Human gut microbiome

In vitro: Short-term supplementation of celecoxib-shifted butyrate production on a simulated model of the gut microbial ecosystem and ameliorated in vitro inflammation – Emma Hernandez-Sanabria et al. – npj Biofilms and Microbiomes

Review: Crosstalk Between Gut Microbiota and Innate Immunity and Its Implication in Autoimmune Diseases – Yuhao Jiao et al. – Frontiers in Immunology

An empirically derived method for measuring human gut microbiome alpha diversity: Demonstrated utility in predicting health-related outcomes among a human clinical sample – Sarah L. Hagerty et al. – PLoS One

Proof-of-concept study of the efficacy of a microbiota-directed complementary food formulation (MDCF) for treating moderate acute malnutrition – Ishita Mostafa et al. – BMC Public Health

Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation – Jonathan U. Peled et al. – New England Journal of Medicine

Human multi-site microbiome

Age-Related Variation of Bacterial and Fungal Communities in Different Body Habitats across the Young, Elderly, and Centenarians in Sardinia – Lu Wu et al. – mSphere

Response of the human gut and saliva microbiome to urbanization in Cameroon – Ana Lokmer et al. – Scientific Reports

The gut-microbiota-brain axis

Therapeutic Effects of the In Vitro Cultured Human Gut Microbiota as Transplants on Altering Gut Microbiota and Improving Symptoms Associated with Autism Spectrum Disorder – Kainan Chen et al. – Microbial Ecology

Built environment microbiome

A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes – Anders B. Nygaard et al. – Scientific Reports


Spatial metabolomics of in situ host–microbe interactions at the micrometre scale – Benedikt Geier et al. – Nature Microbiology

Global chemical effects of the microbiome include new bile-acid conjugations – Robert A. Quinn et al. – Nature

Animal experiments

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

Growth hormone deficiency and excess alter the gut microbiome in adult male mice – Elizabeth A Jensen et al. – Endocrinology

Dissociation of Adaptive Thermogenesis from Glucose Homeostasis in Microbiome-Deficient Mice – Tibor L. Krisko et al. – Cell Metabolism

Fecal IgA Levels Are Determined by Strain-Level Differences in Bacteroides ovatus and Are Modifiable by Gut Microbiota Manipulation – Chao Yang et al. – Cell Host & Microbe

Animal microbiome

Can rumen bacteria communicate to each other? – Mi-Young Won et al. – Microbiome

Entomopathogenic nematode-associated microbiota: from monoxenic paradigm to pathobiome – Jean-Claude Ogier et al. – Microbiome

The canine oral microbiome: variation in bacterial populations across different niches – Avika Ruparell et al. – BMC Microbiology

Evolutionary analysis of Mycobacterium bovis genotypes across Africa suggests co-evolution with livestock and humans – Osvaldo Frederico Inlamea et al. – PLoS NTD

Nanopore sequencing of microbial communities reveals the potential role of sea lice as a reservoir for fish pathogens – Ana Teresa Gonçalves et al. – Scientific Reports

Plant, root and soil microbiome

Insights on aquatic microbiome of the Indian Sundarbans mangrove areas – Paltu Kumar Dhal et al. – PLoS One

Ganoderma lucidum cultivation affect microbial community structure of soil, wood segments and tree roots – Fei Ren et al. – Scientific Reports

Effect of long-term destocking on soil fungal functional groups and interactions with plants – Jie Wang et al. – Plant and Soil

Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters – Zachary Liechty et al. – mSystems

Fungal diversity and community composition of wheat rhizosphere and non-rhizosphere soils from three different agricultural production regions of South Africa – Magalane Pheladi Gqozo et al. – Applied Soil Ecology

Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat – Adam Ossowicki & Vittorio Tracanna et al. – Proceedings of the Royal Society B

Industrial development as a key factor explaining variances in soil and grass phyllosphere microbiomes in urban green spaces – Zhen-Zhen Yan et al. – Environmental Pollution

Plant communities mediate the interactive effects of invasion and drought on soil microbial communities – Catherine Fahey et al. – The ISME Journal

Water and extremophile microbiome

Methyl t-butyl ether-degrading bacteria for bioremediation and biocontrol purposes – Giada d’Errico et al. – PLoS One

Uncovering microbial responses to sharp geochemical gradients in a terrace contaminated by acid mine drainage – Rui Xu et al. – Environmental Pollution

Snapshot: Microbial Extremophiles – Amy K. Schmid et al. – Cell

Denitrification performance and microbial communities of solid-phase denitrifying reactors using poly (butylene succinate)/bamboo powder composite – Wanhe Qi et al. – Bioresource Technology

Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning – Johanne Aubé et al. – Microbial Ecology

Role of microbial diversity for sustainable pyrite oxidation control in acid and metalliferous drainage prevention – Omy T. Ogbughalu et al. – Journal of Hazardous Materials

Phages and viruses

** Coronavirus research highlights – BMC

Fecal Viral Community Responses to High-Fat Diet in Mice – Anjelique Schulfer et al. – mSphere


Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens – Richard M. Leggett et al. – Nature Microbiology

Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities – John Beaulaurier et al. – Genome Research


Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing – Karel Břinda et al. – Nature Microbiology

Microbes in the news

Tough microbe’s DNA could be a lasting archive – Steve Nadis – Science

How Bacteria Can ‘Sculpt The Gut’ – Maya Trabulsi – KPBS

The bee microbiome can fight back against fungi that cause Colony Collapse Disorder – Lauren Sara McKee – Massive Science

Ancient gut microbiomes shed light on human evolution – Newswise

Launch of the Marine Microbiome Roadmap – NIOZ

Understanding Microbiome Resilience on a Changing Planet – Michigan State University

Adaptations in gut microbes helped our ancestors thrive in new geographical territories: Study – New Kerala

Scientists Announce VIRGO, First Comprehensive Gene Catalog To Decode the Vaginal Microbiome – PR Newswire

Metabolomics Reveals Connection Between Gut Microbiome and Blood – Metabolon

Study shows universally positive effect of cover crops on soil microbiome – Phys.org

New Center of Microbiome Science is in the works at Ohio State – Emily Caldwell – Ohio State University News

Common diseases may be communicable through microbiome, says UBC researcher – Stephanie Blain – The Ubyssey

The microbes in your mouth, and a reminder to floss and go to the dentist – Science Daily

For Your Microbiome, How You Eat Could Be As Important As What You Eat – Technology Networks

Study: Infectious gut bacteria may predict UTI risk – Sue Treiman – Cornell Chronicle

The Best Way to Avoid Getting Sick Is to Wash Your Hands — But You’re Probably Doing It Wrong – Bojana Galic – Live Strong

Microbes on the market

DuPont carries on microbiome momentum with metabolic disease collaboration – Will Chu – Nutraingredients

Non-microbiology picks

Invest 5% of research funds in ensuring data are reusable – Barend Mons – Nature


February 18, 2020

Highlights for today’s Digest: a study takes us deep into bacterial community of the dermal compartment of the skin, skin microbiota predicts chronological age most accurately, and a review on network analyses using multi-omics data. Enjoy!

General microbiology

A biphasic growth model for cell pole elongation in mycobacteria – Mélanie T. M. Hannebelle et al. – Nature Communications

Press: Bacteria under the microscope: A new growth model for tuberculosis – Lionel Pousaz, Ecole Polytechnique Federale de Lausanne – Phys.org

Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem – Xinyu Zhu et al. – Microbiome

Antimicrobial resistance

Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli – afael Patiño-Navarrete et al. – Genome Medicine

Pregnancy and early life

The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months – M Isabel Ordiz et al. – The American Journal of Clinical Nutrition

Human skin microbiome

** Universal Dermal Microbiome in Human Skin – Lene Bay et al. – mBio

Human cancer microbiome

Opinion: The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View – Joao B. Xavier et al. – Trends in Cancer

Human gut microbiome

Interactions between the gut microbiome and host gene regulation in cystic fibrosis – Gargi Dayama et al. – Genome Medicine

Human multi-site microbiome

Review: Blood Microbiota and Circulating Microbial Metabolites in Diabetes and Cardiovascular Disease – Ganesan Velmurugan et al. – Trends in Endocrinology & Metabolism

** Human Skin, Oral, and Gut Microbiomes Predict Chronological Age – Shi Huang et al. – mSystems

Press: Human Skin, Oral Microbiomes Can Estimate People’s Ages to Within Few Years – GenomeWeb

Animal experiments

Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine – Said R. Bogatyrev et al. – Microbiome

Mouse: It’s the fiber, not the fat: significant effects of dietary challenge on the gut microbiome – Kathleen E. Morrison et al. – Microbiome

Animal microbiome

Trait-Based Comparison of Coral and Sponge Microbiomes – Cara L. Fiore et al. – Scientific Reports

Plant, root and soil microbiome

Functional relationships between aboveground and belowground spinach (Spinacia oleracea L., cv. Racoon) microbiomes impacted by salinity and drought – A. Mark Ibekwe et al. – Science of the Total Environment

Water and extremophile microbiome

Constraints on microbial communities, decomposition and methane production in deep peat deposits – Laurel A. Kluber et al. – PLoS One

Machine learning-aided analyses of thousands of draft genomes reveal specific features of activated sludge processes – Lin Ye et al. – Microbiome

Phages and viruses

Pearls: Virus interactions with bacteria: Partners in the infectious dance – Ursula Neu & Bernardo A. Mainou – PLoS Pathogens

Coronavirus: hospitals must learn from past pandemics – Nahid Bhadelia – Nature

Review: Phage diversity, genomics and phylogeny – Moïra B. Dion et al. – Nature Reviews Microbiology


Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil – Pauline C. Göller et al. – Microbiome

Review: Combining omics technologies with CRISPR-based genome editing to study food microbes – Meichen Pan & Rodolphe Barrangou – Current Opinion in Biotechnology

Complete, closed bacterial genomes from microbiomes using nanopore sequencing – Eli L. Moss et al. – Nature Biotechnology

Press: Closing bacterial genomes from the human gut microbiome using long-read sequencing – Dylan Maghini – Nature Bioengineering Community


A pipeline for targeted metagenomics of environmental bacteria – Anissa Grieb et al. Microbiome

** Review: Network analyses in microbiome based on high-throughput multi-omics data – Zhaoqian Liu et al. – Briefings in Bioinformatics

Microbes in the news

Getting the Band (of Microbes) Back Together – Jessica Messier – Worcester Polytechnic Institute

Gut microbe imbalance may stunt CF babies’ growth – Leila Gray – University of Washington

The Big Idea: The Microbiome – Purdue University

Moscow’s Subway Microbiome Looks Similar to that of New York’s – GenEngNews

A guide to caring for the Indian gut – Cherylann Mollan – Hindustan Times

February 12, 2020

This Wednesday, read about the microbiome in “flammable ice”, gastric bypass surgery in a rat model, virulence genes of the coral reef phage, and more. Happy reading!

Gut microbiome

Changes in microbiome and metabolomic profiles of fecal samples stored with stabilizing solution at room temperature: a pilot study– Mi Young Lim — Scientific Reports

Fecal microbiota transplantation to maintain remission in Crohn’s disease: a pilot randomized controlled study – Harry Soko – Microbiome

Identification of Clostridioides difficile-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly – Sudeep Ghimire – mySystems

Neonatal microbiota development and the effect of early life antibiotics are determined by two distinct settler types – Anat Eck – plosOne

Oral Microbiome

Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study – Zachary M. Burcham – Scientific Reports

Sub-species niche specialization in the oral microbiome is associated with nasopharyngeal carcinoma risk – Justine W. Debelius – bioRxiv

Animal experiments

*Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss – Sven-Bastiaan Haange – Microbiome

Growth phase-dependent responses of an in vitro gut microbiome to metformin – Zikai Hao – bioRxiv

Ursolic acid improves the bacterial community mapping of the intestinal tract in liver fibrosis mice – Sizhe Wan – bioRxiv

Animal microbiome

Beef cattle that respond differently to fescue toxicosis have distinct gastrointestinal tract microbiota – Lucas R Koester – bioRxiv

Variation in gut bacterial composition is associated with Haemonchus contortus parasite infection of sheep – Md. Abdullah Al Mamun – Animal microbiome

Water microbiome

Microbial diversity, ecological networks and functional traits associated to materials used in drinking water distribution systems – Isabel Douterelo – Water Research

Diverse Arctic lake sediment microbiota shape methane emission temperature sensitivity – Joanne B. Emerson – bioRxiv

Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities – Eslam O. Osman – Microbiome

Extremophile microbiome

*Evidence in the Japan Sea of microdolomite mineralization within gas hydrate microbiomes – Glen T. Snyder – Scientific Reports

Textile waste and microplastic induce activity and development of unique hydrocarbon-degrading marine bacterial communities – Elsa B. Girard – bioRxiv

Plant/root/soil microbiome

Maize (Zea mays L. Sp.) varieties significantly influence bacterial and fungal community in bulk soil, rhizosphere soil, and phyllosphere – Xiao Kong – FEMS Microbiology Ecology

A Small Effort for Researchers, a Big Gain for Soil Metaproteomics– Marco Chiapello – Frontiers in Microbiology

Viruses and phages

*Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes – Cynthia B. Silveira – BMC Genomics

Profiling of Human Gut Virome with Oxford Nanopore Technology – Jiabao Cao – bioRxiv


MICHELINdb: a web-based tool for mining of helminth-microbiota interaction datasets, and a meta-analysis of current research – Riccardo Scotti – Microbiome

February 1, 2020

Today’s Digest brings you an Outlook collection on human gut microbiome by Nature, a Hi-C investigation of the evolution of the gut microbiota, and be careful with the dust, there’s transferrable antimicrobial genes within!


Reshaping the Microbiome through Nutrition – Nature Conference – San Diego, CA

General microbiology

Commensal Bacteroidetes protect against Klebsiella pneumoniae colonization and transmission through IL-36 signalling – Richard P. Sequeira et al. – Nature Microbiology

** The gut microbiome – Nature Outlook

Antimicrobial resistance

The negative cofactor 2 complex is a key regulator of drug resistance in Aspergillus fumigatus – Takanori Furukawa et al. – Nature Communications

Plasmid-mediated metronidazole resistance in Clostridioides difficile – Ilse M. Boekhoud et al. – Nature Communications

A Common Practice of Widespread Antimicrobial Use in Horse Production Promotes Multi-Drug Resistance – S. Álvarez–Narváez et al. – Scientific Reports

Surveys of knowledge and awareness of antibiotic use and antimicrobial resistance in general population: A systematic review – PLoS One

Antimicrobial resistance patterns and molecular resistance markers of Campylobacter jejuni isolates from human diarrheal cases – Mohamed Elhadidy et al. – PLoS One

Review: Antibiotic resistance: turning evolutionary principles into clinical reality – Dan I Andersson et al. – FEMS Microbiology Reviews

Antibiotic resistome associated with microbial communities in an integrated wastewater reclamation system – Kaifeng Yu et al. – Water Research

Human gut microbiome

** Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation – Eitan Yaffe & David A. Relman – Nature Microbiology

Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease – Nadine Fornelos et al. – Nature Microbiology

Human cancer microbiome

The Influence of Lung Microbiota on Lung Carcinogenesis, Immunity, and Immunotherapy – Ariel G. Ramírez-Labrada et al. – Trends in Cancer

Built environment microbiome

** Mobilizable antibiotic resistance genes are present in dust microbial communities – Sarah Ben Maamar et al. – PLoS Pathogens

Indoor and outdoor airborne bacterial and fungal air quality in kindergartens: seasonal distribution, genera, levels, and factors influencing their concentration – Farhad Mirkhond Chegini et al. – Building and Environment


Targeted metabolomics of pellicle and saliva in children with different caries activity – Annika Schulz et al. – Scientific Reports

Animal experiments

Review: The role of the microbiota in sedentary life style disorders and ageing: Lessons from the animal kingdom – P.W. O’Toole & P.G. Shiels – Journal of Internal Medicine

Animal microbiome

Dietary effects on gut microbiota of the mesquite lizard Sceloporus grammicus (Wiegmann, 1828) across different altitudes – Nina Montoya-Ciriaco et al. – Microbiome

Late weaning is associated with increased microbial diversity and Faecalibacterium prausnitzii abundance in the fecal microbiota of piglets – Francesca Romana Massacci et al. – Animal Microbiome

Plant, root and soil microbiome

Effects of soil chemical properties and fractions of Pb, Cd, and Zn on bacterial and fungal communities – Xiaomei Pan et al. – Science of the Total Environment

Resilience of the microbial communities of semiarid agricultural soils during natural climatic variability events – Lumarie Pérez-Guzmán et al. – Applied Soil Ecology

Effects of microbial inoculants on the fermentation characteristics and microbial communities of sweet sorghum bagasse silage – Miaoyin Dong et al. – Scientific Reports

Water and extremophile microbiome

Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing – Genevieve L. Fernandes et al. – Frontiers in Microbiology

Ionic Liquid Enriches the Antibiotic Resistome, Especially Efflux Pump Genes, Before Significantly Affecting Microbial Community Structure – Xiaolong Wang et al. – Environmental Science & Technology

Methane yield enhancement of mesophilic and thermophilic anaerobic co-digestion of algal biomass and food waste using algal biochar: Semi-continuous operation and microbial community analysis – Le Zhang et al. – Bioresource Technology

Characterization and co-occurrence of microbial community in epiphytic biofilms and surface sediments of wetlands with submersed macrophytes – Yuansi Liu et al. – Science of the Total Environment

Phages and viruses

** Giant virus diversity and host interactions through global metagenomics – Frederik Schulz et al. – Nature

Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China – Bingqian Qu et al. – PLoS One

Outbreak of Pneumonia of Unknown Etiology in Wuhan China: the Mystery and the Miracle – Hongzhou Lu et al. – Journal of Medical Virology


Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing – Andrei Prodan et al. – PLoS One

Microbes in the news

Walnuts May Benefit Gut Bacteria and Improve Heart Health – Karina Lichtenstein – Medicine Net

How to create living art with microbes – Eugenia Angulo – BBVA OpenMind