Category Archives: Metagenomics & Bioinformatics

May 7, 2020

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Good morning! There’s a particularly broad collection of microbiome papers to share with you today, from the bacteria that hang onto wounds after debridement to the biofilms that form in the ancient ruins of a town buried by the eruption of Mount Vesuvius. A few unusual highlights include the sexually transmitted microbiome of bedbugs and the gut microbes that colonize a sea cucumber after it grows up, remove its own digestive tract and grows a new one. Some interesting new software tools are hiding in the “Bioinformatics” section at the bottom as well.

General microbiome

Intracellular Staphylococcus aureus persisters upon antibiotic exposure, Frédéric Peyrusson et al., Nature Communications

Human respiratory microbiome

Investigation of the human nasal microbiome in persons with long- and short-term exposure to methicillin-resistant Staphylococcus aureus and other bacteria from the pig farm environment, Md Zohorul Islam et al., PLOS ONE

Human skin microbiome

Microbial predictors of healing and short-term effect of debridement on the microbiome of chronic wounds, Samuel Verbanic et al., npj Biofilms and Microbiomes

Human gut microbiome

Systemic short chain fatty acids limit antitumor effect of CTLA-4 blockade in hosts with cancer, Clélia Coutzac et al., Nature Communications

Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity, Mathilde Payen et al., Blood Advances

Animal experiments

Preprint: Metagenomic alterations in gut microbiota precede and predict onset of colitis in the IL10 gene-deficient murine model, Miyoshi and Lee et al., bioRxiv

Dietary Fiber Protects against Diabetic Nephropathy through Short-Chain Fatty Acid–Mediated Activation of G Protein–Coupled Receptors GPR43 and GPR109A, Yan Jun Li et al., Journal of the American Society of Nephrology

Probiotic strain Lactobacillus plantarum YYC-3 prevents colon cancer in mice by regulating the tumour microenvironment, Yuanchun Yue et al., Biomedicine & Pharmacotherapy

Effect of stevia on the gut microbiota and glucose tolerance in a murine model of diet-induced obesity, Sarah L. Becker et al., FEMS Microbiology Ecology

Animal microbiome

Sea cucumber intestinal regeneration reveals deterministic assembly of the gut microbiome, Brooke L. Weigel, Applied and Environmental Microbiology

Mating changes the genital microbiome in both sexes of the common bedbug Cimex lectularius across populations, Sara Bellinvia et al., Proceedings of the Royal Society B

Plant, root, and soil microbiome

Mutualist and pathogen traits interact to affect plant community structure in a spatially explicit model, John W. Schroeder et al., Nature Communications

Preprint: Seasonal dynamics of methane cycling microbial communities in Amazonian floodplain sediments, Julia B. Gontijo et al., bioRxiv

Preprint: Community succession of the grapevine fungal microbiome in the annual growth cycle, Liu and Howell, bioRxiv

Characterizing changes in soil microbiome abundance and diversity due to different cover crop techniques, Wang and Wu et al., PLOS ONE

Preprint: Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field, Selma Cadot et al., bioRxiv

Water and extremophile microbiome

The role of changing temperature in microbial metabolic processes during permafrost thaw, Komi S. Messan et al., PLOS ONE

Built environment

Microbial biofilm community structure and composition on the lithic substrates of Herculaneum Suburban Baths, De Natale and Mele et al., PLOS ONE

Probiotics/prebiotics

Comparative effectiveness of probiotic-based formulations on cecal microbiota modulation in broilers, Denise R. Rodrigues et al., PLOS ONE

Phages and viruses

Weirdo19ES is a novel singleton mycobacteriophage that selects for glycolipid deficient phage-resistant M. smegmatis mutants, Cristian Alejandro Suarez et al., PLOS ONE

Bioinformatics

Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease, Tataru and David, PLOS Computational Biology

Sequence count data are poorly fit by the negative binomial distribution, Stijn Hawinkel et al., PLOS ONE

Preprint: sPepFinder expedites genome-wide identification of small proteins in bacteria, Li and Chao, bioRxiv

Logicome Profiler: Exhaustive detection of statistically significant logic relationships from comparative omics data, Fukunaga and Iwasaki, PLOS ONE

May 2nd, 2020

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Another month has passed! Hope everyone is staying at home and being well. Today’s highlights include a paper applying NMR to monitor neonatal metabolic adaptations, how oil influence microbial community assembly off the Gulf of Mexico and a preprint for a Bayesian Multi-task method to identify global microbiome associations.

COVID-19 Articles 

Why the Coronavirus Is So Confusing – Ed Yong – The Atlantic

Aerodynamic analysis of SARS-CoV-2 in two Wuhan hospitals – Liu & Ning et al. – Nature

Human microbiome

Fucosidases from the human gut symbiont Ruminococcus gnavus – Wu & Rebello et al. – Cellular and Molecular Life Sciences

Temporal Dysbiosis of Infant Nasal Microbiota Relative to Respiratory Syncytial Virus Infection – Grier et al. – bioRxiv **preprint**

Sex-specific Alterations in the Urinary and Tissue Microbiome in Therapy-naïve Urothelial Bladder Cancer Patients – Pederzoli et al.  – European Urology Oncology

Microbiome and Metabolomics 

Metabolic changes in early neonatal life: NMR analysis of the neonatal metabolic profile to monitor postnatal metabolic adaptations – Georgakopoulou, I., Chasapi, S.A., Bariamis, S.E. et al – Metabolomics

Analyzing the impact of Mycobacterium tuberculosis infection on primary human macrophages by combined exploratory and targeted metabolomics – Vrieling & Kostidis et al. – Nature Scientific Reports

Soil microbiome

Structural and microbial evidence for different soil carbon sequestration after four-year successive biochar application in two different paddy soils – Bi & Cai et al. – Chemosphere

Soil pH and C/N ratio determines spatial variations in soil microbial communities and enzymatic activities of the agricultural ecosystems in Northeast China: Jilin Province case – Xu et al. – Applied Soil Ecology

Animal microbiome

Viral metagenomics revealed diverse CRESS-DNA virus genomes in faeces of forest musk deer – Liu & Wang et al. – Virology Journal

Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation – Bowen & Cormican et al. – PLOS One

Microbiomes of the built environment 

Influence of oil, dispersant, and pressure on microbial communities from the Gulf of Mexico – Noirungsee et al. – Nature Scientific Reports

Passenger-surface microbiome interactions in the subway of Mexico City – Vargas-Robles et al.  – bioRxiv **preprint**

Pathogens 

Intra-species signaling between Pseudomonas aeruginosa genotypes increases production of quorum sensing controlled virulence factors – Mould et al. – bioRxiv **preprint**

Statistics and bioinformatics 

A Bayesian Multi-Task Approach for Detecting Global Microbiome Associations – Hatami et al. – bioRxiv (soon to be published in Bioinformatics) **preprint**

Extremophiles

Genomic sequencing of Gracilibacillus dipsosauri reveals key properties of a salt-tolerant a-amylase – Deutch & Yang – Antonie van Leeuwenhoek

Aquatic environments  

Cyanobacteria in inland waters: new monitoring, reporting, modelling and ecological research – Mitrovic et al. – Marine & Freshwater Research **review**

Contrast diversity patterns and processes of microbial community assembly in a river-lake continuum across a catchment scale in northwestern China – Tang et al. – Environmental Microbiome

Microbiome in the News

Coffee plants have a small but consistent core microbiome of fungi and bacteria – American Phytopathological Society – EurekAlert!

May 1, 2020

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Greetings from Durham, NC!

Hope everyone is doing well and staying healthy. Today’s digest includes several host-microbiome studies, environmental microbiome studies, and an intriguing EurekAlert news article.
In this light digest of today, I wanted to highlight a cool review about correlation of the oral microbiome with children’s health and a very interesting article on cell wall architecture of the gram-positive bacteria.
COVID-19 pandemic has opened a sort of Pandora’s box filled with great science along with pseudoscience. So, the digest has these two great articles from Nature: one about chloroquine and other about the race for coronavirus vaccines.
Staying at home is difficult for everyone, here is a fun activity to do: coloring space microbes book.

Stay Safe and entertained at home!!!!

COVID-19 news articles

The race for coronavirus vaccines: a graphical guide – Callaway – Nature

Chloroquine hype is derailing the search for coronavirus treatments – Ledford – Nature

General microbiome
*The architecture of the Gram-positive bacterial cell wall– Pasquina-Lemonche et al. – Nature

Pregnancy and early life
Maternal H. pylori is associated with differential fecal microbiota in infants born by vaginal delivery – Hernandez et al. – Scientific Reports

Metabolic Effects of Bovine Milk Oligosaccharides on Selected Commensals of the Infant Microbiome—Commensalism and Postbiotic Effects – Jakobsen et al. – Metabolites

Multi-site human microbiome
*Review: Oral microbiome: possible harbinger for children’s health – Xiao et al. – Nature International Journal of Oral Science

Animal microbiome
Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation – Bowen et al. – PLOS ONE

Plant, root, and soil microbiome
Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean – Han et al. – The ISME Journal

Water and extremophile microbiome
Review: Exopolysaccharides from marine bacteria: production, recovery and applications – Dave et al. – Environmental Sustainability

Stromatolitic digitate sinters form under wide‐ranging physicochemical conditions with diverse hot spring microbial communities – Sriaporn et al. – gebiology

Built environment
Comparative analysis of bacterial community and functional species in oil reservoirs with different in situ temperatures – Tian et al. – International Microbiology

Bioinformatics
Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions – Medlock et al. – PLOS Computational Biology

Review: The National Microbiome Data Collaborative: enabling microbiome science – Wood-Charlson et al. – Nature Reviews Microbiology

Probiotics / prebiotics
Lactobacillus plantarum NA136 ameliorates nonalcoholic fatty liver disease by modulating gut microbiota, improving intestinal barrier integrity, and attenuating inflammation – Zhao et al. -Applied Microbiology and Biotechnology

Microbes in the news
Scientists explore links between genetics, gut microbiome and memory – DOE/PACIFIC NORTHWEST NATIONAL LABORATORY

April 21, 2020

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Hello all from another new Microbiome Digest volunteer! This post is coming to you straight from the heart of New York City – being surrounded everywhere by COVID-19 (and related research!), it’s been good to get back into the microbiome world 🙂 I love all things microbiology but am partial to bacteria, especially multidrug-resistant pathogens and communities involved in biological nutrient removal/recovery from waste.

Today’s roundup is heavy on the soil and environmental microbiomes and some interesting preprints, with some unique finds – indigenous yeasts in winemaking, gut microbiomes after dietary interventions in adult dogs, and much more!

Human gut microbiome

Characterization of Gut Microbiota in Hospitalized Patients with Clostridioides difficile Infection – Bahareh Vakili – Current Microbiology

Animal experiments
Genetic and metabolic links between the murine microbiome and memory – Jian-Hua Mao – Microbiome

A human-origin probiotic cocktail ameliorates aging-related leaky gut and inflammation via modulating microbiota-taurine-tight junction axis
Shokouh Ahmadi – JCI Insight

Animal microbiome

Preprint: CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content – Maxime Borry – bioRxiv

Phylogenetic analysis of intestinal microbiota reveals novel Mycoplasma phylotypes in salmonid species – Brenda Mora-Sánchez – Microbial Pathogenesis

Rapid Reconstitution of the Faecal Microbiome after Extended Diet-Induced Changes Indicate a Stable Gut Microbiome in Healthy Adult Dogs – David Allaway – Applied and Environmental Microbiome

Plant, root, and soil microbiome

Review: Harnessing rhizosphere microbiomes for drought-resilient crop production – Franciska T. de Vries – Science

Book Chapter: Endophytic Actinomycetes-Mediated Modulation of Defense and Systemic Resistance Confers Host Plant Fitness Under Biotic Stress Conditions – Waquar Akhter Ansari – Microbial Versatility in Varied Environments

Elevated CO2 mitigates the negative effect of CeO2 and Cr2O3 nanoparticles on soil bacterial communities by alteration of microbial carbon use – Jipeng Luo – Environmental Pollution

Periodic waterlogging consistently shapes agricultural soil microbiomes by promoting specific taxa – Florian Gschwend – Applied Soil Ecology

Food microbiology

Review:Indigenous yeasts: Emerging Trends and Challenges in winemaking – Iliada K. Lappa – Current Opinion in Food

Ecology of lactobacilli present in Italian cheeses produced from raw milk
Christian Milani – Applied and Environmental Microbiology

Probiotics / prebiotics
Probiotic supplementation improves cognitive function and mood with changes in gut microbiota in community-dwelling elderly: A randomized, double-blind, placebo-controlled, multicenter trial – Chong-Su Kim – The Journals of Gerontology

Phages and viruses
Intestinal microbiome‐macrophage crosstalk contributes to cholestatic liver disease by promoting intestinal permeability – Anna Isaacs-Ten – Hepatology

Bioinformatics
Preprint: hogwash: Three Methods for Genome-Wide Association Studies in Bacteria – Katie Saund – bioRxiv

Mycobiome

Preprint: Mycobiome analysis in fungal Infected formalin-fixed and paraffin-embedded tissues for identification of pathogenic fungi: A pilot study – Taebum Lee – bioRxiv

Host-Pathogen Interactions
Preprint: Human GBP1 differentially targets Salmonella and Toxoplasma to license recognition of microbial ligands and caspase-mediated death – Daniel Fisch – bioRxiv

Preprint: Mechanical competition triggered by innate immune signaling drives the collective extrusion of bacterially-infected epithelial cells – Effie E. Bastounis – bioRxiv

Microbes on the market

Genome & Company receives FDA IND clearance for GEN-001, its first anti-cancer microbiome therapeutic (Press Release, BioSpace)

April 19, 2020

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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

Bioinformatics

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

Techniques

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

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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

Bioinformatics

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

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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.

COVID-19
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.

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

Techniques
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 9, 2020

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Good morning! There’s a diverse set of microbiome papers to share today, ranging from the human microbiome in Lynch Syndrome to the microbes that flavor wine and degrade paintings in art galleries. You may also want to check out the recent news that popular video game Borderlands 3 is introducing a new mini-game that prompts players to help “map” the human gut microbiome—technical details are hard to come by, but it appears to be alignment related. There is also a study that found more than 20 percent of recently published metagenomes are not accessible.

In addition, Microbiome Data Congress 2020 will be held online on May 6 and is offering free registration through tomorrow (Friday, April 10). Speakers include human microbiome researcher Dr. Nikos Kyrpides of the (U.S.) DOE Joint Genome Institute and soil microbiologist Dr. Kari Dunfield of the University of Guelph.

Human gut microbiome

Structure of the Mucosal and Stool Microbiome in Lynch Syndrome, Yan Yan et al., Cell Host & Microbe

Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome, Tam and Filho et al., PLOS ONE

The gut microbiome but not the resistome is associated with urogenital schistosomiasis in preschool-aged children, Derick N. M. Osakunor et al., Communications Biology

Perspective: Developing a new class of engineered live bacterial therapeutics to treat human diseases, Mark R. Charbonneau et al., Nature Communications

Review: The gut mycobiome: The overlooked constituent of clinical outcomes and treatment complications in patients with cancer and other immunosuppressive conditions, Galloway-Peña and Kontoyiannis, PLOS Pathogens

Intestinal enteroids recapitulate the effects of short-chain fatty acids on the intestinal epithelium, Sarah C. Pearce et al., PLOS ONE

Animal experiments

A combination of monosodium glutamate and high-fat and high-fructose diets increases the risk of kidney injury, gut dysbiosis and host-microbial co-metabolism, Thatsanapong Pongking et al., PLOS ONE

Plant, root, and soil microbiome

Preprint: Vineyard ecosystems are structured and distinguished by fungal communities impacting the flavour and quality of wine, Di Liu et al., bioRxiv

Bacterial community composition of vermicompost-treated tomato rhizospheres, Juana Munoz-Ucros et al., PLOS ONE

Field Performance of Mixtures of Pseudomonas and Bacillus spp. in Managing Papaya Ringspot Virus Disease and their Effect on Plant Defense Enzyme Activity, Ranasinghe and De Costa, Tropical Agricultural Research

Built environment

Detection of potential biodeterioration risks for tempera painting in 16th century exhibits from State Tretyakov Gallery, Alexander Zhgun et al., PLOS ONE

Microbiome and antibiotic resistome in household dust from Beijing, China, Long-Jun Ding et al., Environment International

Preprint: Microbial dark matter driven degradation of carbon fiber polymer composites, Adam M. Breister et al., bioRxiv

Phages and viruses

Preprint: Primate phageomes are structured by superhost phylogeny and environment, Jan-Frederik Gogarten et al., bioRxiv

Bioinformatics

PIA: More Accurate Taxonomic Assignment of Metagenomic Data Demonstrated on sedaDNA From the North Sea, Becky Cribdon et al., Frontiers in Ecology and Evolution

Techniques

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

Science, publishing, and career

Every fifth published metagenome is not available to science, Eckert, Di Cesare and Fontaneto et al., PLOS Biology

April 5, 2020.

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All the break-neck speed with which the progress that is happening today in tracking, detecting and treating the disease, like everything else, is owed in part to the giants whose shoulders we’re standing on. One such thing is the usage of serum (from recovered patients or derived elsewhere) for treatment. So, as a little tribute, I would like to share with you today, on the birthday of Dr. Hattie Elizabeth Alexander (born April 5, 1901), the information that she pioneered the work in using anti-influenzal rabbit serums to treat the then always-fatal influenzal meningitis (effectively bringing down the fatality rate to 20%!), and was also sone of the very first to study bacterial mutations that come along with antibiotic resistance !

So we’ve come a long way and are forging our way forward. Here are a few interesting articles that are slowly pushing this boundary, a piece at a time.

COVID-19

From PREDICT to prevention, one pandemic later – Colin J Carlson – The Lancet.

Human Microbiome

Review: Risk factors associated with gastric malignancy during chronic Helicobacter pylori infection – Ami Y Seegar – Medical Research Archives.

Review: From Association to Causality: the Role of the Gut Microbiota and Its Functional Products on Host Metabolism – Ara Koh – Molecular Cell.

Pregnancy and Early Life

Breast Milk and Microbiota in the Premature Gut: A Method of Preventing Necrotizing Enterocolitis – Orga PL et al – Karger.

Human Brain and Microbiome

Book: Integrative and Functional Medical Nutrition Therapy. Chapter: The Microbiome and Brain Health – Sharon L. Norling -Springer

Animal Experiments


Integrated omics profiling of dextran sodium sulfate-induced colitic mice supplemented with Wolfberry (Lycium barbarum). Wanping Aw et al – NPJ Science of Food.

Botany

Rhizobacteriome: Promising Candidate for Conferring Drought Tolerance in Crops – Vinod Yadav et al – Journal of Pure Applied Microbiology

Legionella species: A potential problem associated with rain water harvesting systems? – Judith A Taylor et al – SAGE Journals

Bioinformatics

Applications of Machine Learning Predictive Models in the Chronic Disease Diagnosis – Gopi Battineni et al – Journal of Personalized Medicine

PS: I know, I am with you on this — the lockdown isn’t ideal. But we are also the generation, who for the first time can end articles signing off as “Stay Safe and Wash Your Hands” and manage to prevent a large proportion of its species from suffering / dying. Isn’t that crazy! Have a great day!

More information on Dr. Hattie Elizabeth Alexander — here and here.

April 4, 2020

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Good morning and salutations from Singapore! This is the first digest that I’m contributing for the blog, so I hope my selections are interesting to you all! Today’s digest begins with some recent COVID-19 pre-prints, before getting into papers on a diverse range of microbiome-related topics. Highlights today include a study on cats potentially harbouring SARS-CoV-2 (nooo…), the effect of C-section birth on the vaginal microbiota of adult women, and the impact of the virome on biogeochemical cycling in Lake Baikal.

COVID-19

Preprint: Characterization and treatment of SARS-CoV-2 in nasal and bronchial human airway epithelia – Pizzorno et al.

* Preprint: SARS-CoV-2 neutralizing serum antibodies in cats: a serological investigation – Zhang et al.

Preprint: Direct RNA sequencing and early evolution of SARS-CoV-2 – Taiaroa et al.

General microbiome

Review: Microbiota and metabolites in rheumatic diseases – Tong et al. – Autoimmunity Reviews

Human respiratory microbiome

Preprint: Distinctive airway microbial ecology of smokers and asthmatics – Turek et al.

Microbial burden and viral exacerbations in a longitudinal multicenter COPD cohort – Bouquet et al. – Respiratory Research

Human gut microbiome

An in vitro evaluation of the effects of different statins on the structure and function of human gut bacterial community – Zhao et al. – PLoS ONE

Human vaginal microbiome

* A cross-sectional pilot study of birth mode and vaginal microbiota in reproductive-age women – Stennett et al. – PLoS ONE

Animal experiments

Polysaccharide extracted from WuGuChong reduces high-fat diet-induced obesity in mice by regulating the composition of intestinal microbiota – Wang et al. – Nutrition & Metabolism

Animal microbiome

Intestinal microbes: an axis of functional diversity among large marine consumers – Scott et al. – Proceedings of the Royal Society B

Plant, root, and soil microbiome

The response of soil and phyllosphere microbial communities to repeated application of the fungicide iprodione: Accelerated biodegradation or toxicity? – Katsoula et al. – FEMS Microbiology Ecology

Divergent patterns of microbial community composition shift under two fertilization regimes revealed by responding species – Yao et al. – Applied Soil Ecology

Water and extremophile microbiome

* Preprint: New Viral Biogeochemical Roles Revealed Through Metagenomic Analysis of Lake Baikal – Coutinho et al.

Bioinformatics

Ten simple rules for providing effective bioinformatics research support – Kumuthini et al. – PLoS Computational Biology

Finally, remember that physical isolation doesn’t have to mean social isolation. Call someone you haven’t talked to in a while, I’m sure they’ll appreciate it! You’re doing great 😀