Category Archives: Animal microbiome

May 5, 2020

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Events

The Virtual Microbiome Summit – May 19-22, 2020

Multi-site human microbiome

Comparison of microbiomes in ulcerative and normal mucosa of recurrent aphthous stomatitis (RAS)-affected patients – Yang et al. – BMC Oral Health

Human gut microbiome

Gut bacterial ClpB-like gene function is associated with decreased body weight and a characteristic microbiota profile – Arnoriaga-Rodríguez et al. – Microbiome

Preprint: Antibiotics may influence gut microbiome signaling to the brain in preterm neonates – Russell et al. – bioRxiv

Animal experiments

Infection with the sheep gastrointestinal nematode Teladorsagia circumcincta increases luminal pathobionts – Cortés et al. – Microbiome

Techniques

Preprint: A study’s got to know its limitations – Gooch et al. – bioRxiv

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 26, 2020

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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 24, 2020

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Events

Virtual Podium 2020 – Session 5 (Microbiome) – April 24, 2020

Scientific career and work-life balance – April 24, 2020

World Malaria Day – April 25, 2020 – Draws attention to the impact of the disease and (re)urges us to find a way to overcome it once and for all.
Join the #talkingmalaria tweetchat on April 24, 2020 at 12 noon BST.

COVID-19

GRAND CHALLENGE: A billion molecules against COVID-19 – Joint European Disruptive Initiative

General microbiome

Reversibility of propionic acid inhibition to anaerobic digestion: Inhibition kinetics and microbial mechanism – Youl Han – Chemosphere

Responses of microbial structures, functions, metabolic pathways and community interactions to different C/N ratios in aerobic nitrification – Hongwei Sun – Bioresource Technology

PERSPECTIVE: Cultivating fungal research – Heidi H. Kong – Science

Human microbiome

REVIEW: Microbiota–immune interactions in asthma pathogenesis and phenotype – Nicholas W.Lukacs – Current Opinion in Immunology

CANCER IN TRANSLATION: Microbiome genomics for cancer prediction – Lorenz Adlung – Nature Cancer

Human skin microbiome

BOOK CHAPTER: The wound microbiome – Aayushi Uberoi – In: Wound Healing, Tissue Repair, and Regeneration in Diabetes.

Human gut microbiome

BOOK CHAPTER: Dietary Fiber and Gut Microbiota – Carolina Senés-Guerrero – In: Science and Technology of Fibers in Food Systems

Animal experiments

Effect of in feed administration of different butyrate formulations on Salmonella Enteritidis colonization and cecal microbiota in broilers – Lonneke Onrust – Veterinary Research

Stochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics – Ori Furman – Nature Communications

Sequence variant analysis reveals poor correlations in microbial taxonomic abundance between humans and mice after gnotobiotic transfer – Farnaz Fouladi – ISME Journal

Temporal changes in microbial communities attached to forages with different lignocellulosic compositions in the cattle rumen – Javad Gharechahi – FEMS Microbiology Ecology

Animal microbiome

Host-microbiota interaction helps to explain the bottom-up effects of climate change on a small rodent species – Guoliang Li – ISME Journal

Plant, root, and soil microbiome

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions – Stien Beirinckx – Microbiome

Regulatory relationship between quality variation and environment of Cistanche deserticola in three ecotypes based on soil microbiome analysis – Xiao Sun – Scientific Reports

Effects of biodegradable plastic film mulching on soil microbial communities in two agroecosystems – Sreejata Bandopadhyay – PeerJ

Water microbiome

Total Microbial Activity and Sulfur Cycling Microbe Changes in Response to the Development of Hypoxia in a Shallow Estuary – Yunjung Park – Ocean Science Journal

Built environment

Associations Between Respiratory Infections and Bacterial Microbiome in Student Dormitories in Northern China – Xi Fu – Indoor Air

Bacterial community analysis of floor dust and HEPA filters in air purifiers used in office rooms in ILAS, Beijing – Jianguo Guo – Scientific Reports

Microbes in space

The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation – Camilla Urbaniak – Microbiome

Food microbiology

Insights into the Microbiological Safety of Wooden Cutting Boards Used for Meat Processing in Hong Kong’s Wet Markets: A Focus on Food-Contact Surfaces, Cross-Contamination and the Efficacy of Traditional Hygiene Practices – Patrick T. Sekoai – Microorganisms

Pre-print

MicrobioLink: An integrated computational pipeline to infer functional effects of microbiome-host interactions – Tahila Andrighetti – bioRxiv

Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota – Shirin Moossavi – bioRxiv

Mendelian randomization analysis revealed causal effects from gut microbiota to abdominal obesity – Qian Xu – bioRxiv

A quantitative measure of functional redundancy in microbial ecosystems – Taylor M Royalty – bioRxiv

Host association induces genome changes in Candida albicans which alters its virulence – Amanda C Smith – bioRxiv

Shirin’s non-microbiology picks

CAREER FEATURE: Safely conducting essential research in the face of COVID-19 – Virginia Gewin – Nature

Reaching a Large Urban Undergraduate Population through Microbial Ecology Course-Based Research Experiences – Samantha Parks – Journal of Microbiology & Biology Education

POLICY FORUM: Against pandemic research exceptionalism – Alex John London – Science

WORLD VIEW: On the 50th Earth Day, take collective action for the planet – Emma Marris – Nature

BEHIND THE PAPER: Annotating the unknown: Functional Gene Annotation using Untargeted Metabolomics – Robert Jansen – Nature Microbiology Community

April 23, 2020

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The wave of new microbe enthausiasts keeps coming and with it a light digest for today.  I am writing to you from Bremen, Germany, with a selection including a wheat fungi that changes the wheat leaf microbiome and antimicrobial resistance genes identified by whole metagenome shotgun study of nasopharyngal colonization in South Africa.

There is also an interesting article about species identification errors occurring in context of large sequence collection platforms.
And to mix things up a little bit, at the end of a list you find a paper with amazing microscopy featuring the beautiful parasite Trypanosoma brucei and answering the endless question to how this parasite colonizes its insect host, the tsetse fly.

Human respiratory microbiome

Longitudinal changes in the nasopharyngeal resistome of South African infants using shotgun metagenomic sequencing – Rendani I. Manenzhe – PLOS ONE

Human gut microbiome

Resident microbial communities inhibit growth and antibiotic-resistance evolution of Escherichia coli in human gut microbiome samples – Michael Baumgartner – PLOS BIOLOGY

Animal experiments

Preprint: Comparative analysis of beneficial effects of Vancomycin treatment on Th1- and Th2-biased mice and role of gut microbiota – Pratikshya Ray – bioRxiv

Assessment of dietary supplementation with galactomannan oligosaccharides and phytogenics on gut microbiota of European sea bass (Dicentrarchus Labrax) fed low fishmeal and fish oil based diet – Simona Rimoldi – PLOS ONE

Lactobacillus reuteri attenuated allergic inflammation induced by HDM in the mouse and modulated gut microbes – Lingzhi Li – PLOS ONE

Animal microbiome

Occurrence of Mycoplasma gallisepticum in wild birds: A systematic review and meta-analysis – Anna Sawicka – PLOS ONE

Plant, root, and soil microbiome

A fungal pathogen induces systemic susceptibility and systemic shifts in wheat metabolome and microbiome composition – Heike Seybold – Nature Communications

Phages and viruses

SMOOT libraries and phage-induced directed evolution of Cas9 to engineer reduced off-target activity – Derek Cerchione – PLOS ONE

Bioinformatics

BOLD and GenBank revisited – Do identification errors arise in the lab or in the sequence libraries? – Mikko Pentisaari – PLOS ONE

Science, publishing, and career

A pedagogical approach to science outreach – Marni B. McClure – PLOS BIOLOGY

Judith’s non-microbiology picks

Trypanosoma brucei colonizes the tsetse gut via an immature peritrophic matrix in the proventriculus – Clair Rose – Nature Microbiology

April 22, 2020

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Welcome to another post from a new volunteer! I’m a Ph.D student studying the infant gut microbiome and I’m excited to be volunteering with Microbiome Digest.

There are several preprints today, including another great study from the CHILD cohort. This one is on maternal consumption of artificially sweetened beverages and the infant gut microbiota. There is also a preprint calling for improvement in scientific conferences. Both are highlighted in green.

Pregnancy and early life

Preprint: Consumption of artificially sweetened beverages during pregnancy impacts infant gut microbiota and body mass index – Isabelle Laforest-Lapointe — bioRxiv

Oral microbiome

Preprint: Genotypic and phenotypic characterization of Streptococcus mutans isolated from dental caries – Mohammad Shahnoor Hossain – bioRxiv

Pyruvate secretion by oral streptococci modulates hydrogen peroxide dependent antagonism – Sylvio Redanz – ISME Journal

Synergism between Corynebacterium and Streptococcus sanguinis reveals new interactions between oral commensals – Puthayalai Treerat – ISME Journal

Animal experiments

The gut microbiota response to helminth infection depends on host sex and genotype – Fei Ling – ISME Journal

Animal microbiome

Lipids and small metabolites provisioned by ambrosia fungi to symbiotic beetles are phylogeny-dependent, not convergent – Yin-Tse Huang – ISME Journal

Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP) – Kshitij Tandon – ISME Journal

Plant, root, and soil microbiome

Active sulfur cycling in the terrestrial deep subsurface – Emma Bell – ISME Journal

Preprint: An antagonistic driver of the microbial phyllosphere suppresses infection of Arabidopsis thaliana by the oomycete pathogen Albugo laibachii via a secreted hydrolase – Katharina Eitzen – bioRxiv

Preprint: Grapevine pruning time affects natural wound colonization by wood-invading fungi – Maria del Pilar Martinez-Diz – bioRxiv

Water and extremophile microbiome

Mixotrophy in marine picocyanobacteria: use of organic compounds by Prochlorococcus and Synechococcus – M.C. Muñoz-Marín – ISME Journal

Food microbiology

Preprint: Antibiotic-resistant Salmonella species and Escherichia coli in broiler chickens from farms, abattoirs and open markets in selected districts of Zambia – Nelson Phiri – bioRxiv

Microbes in the news

Breastfeeding may lead to fewer human viruses in infants
https://www.sciencedaily.com/releases/2020/04/200415110452.htm

Science, publishing, and career

Preprint: Evaluating features of scientific conferences: A call for improvements – Sarvenaz Sarabipour – bioRxiv

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 20, 2020

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God morgon!

Good morning from Sweden. To all my friends who have lost the track of time during the quarantine, it is Monday and the beginning of a new week. Today’s digest is a very light one. However, it carries a super interesting preprint that studies the impact of the pandemic on publication speed of different medical journals. The study reports that, on average, the COVID-19 related papers were expedited through the peer-review process at a 49% (up to 80% in case of certain journals) higher pace than the mean pre-pandemic publishing speed (Yes, there is a pre-pandemic and, possibly, a post-pandemic era now). Although this is a controversial topic, I guess the preprint did a very good job of discussing the reasons behind and impact of accelerated publishing.

In my personal opinion, it is great to be able to get valuable scientific information as soon as it is produced. However, as the paper points out, there has to be some sort of trade-off between the quality of a publication and the time taken by the peer-review process. It could be argued that the quarantine measures might have made it easier for some reviewers to focus their attention on the peer-review, making it faster, but there is no information on ‘who’ reviewed these papers. Also, the article highlights what a lot of scholars have been warning about – the amount of post-publishing corrections that these papers would require (more work for Ms Bik!).

What do you think could be the reasons behind this unprecedented celerity of publishing? Could it be the availability of more spare time to review papers? or could this be an instance of politicization of science (as someone pointed out in the comments section of the article)? What could be the impact of this swiftness, both positive and negative, on the scientific realm? Would it be possible, or advisable, to keep up this trend of swift publishing in the post-pandemic era? Let’s discuss in the comments section.

Apart from this highly thought-provoking article, there is another interesting article on the identification of bacterial strains that may promote maize (corn, for my American friends) growth in chilling conditions.

There is another interesting article that tries to establish a link between the gut microbiome and memory. The study focused on microbiome-specific genetic and metabolomic changes that may impact memory. The study was performed in mice.

Enjoy the articles, have a great week, and stay safe!

COVID 19

Preprint: Pandemic Publishing: Medical journals drastically speed up their publication process for Covid-19 – Serge P.J.M. Horbach

Preprint: Coronavirus Infection and PARP Expression Dysregulate the NAD Metabolome: A Potentially Actionable Component of Innate Immunity – Collin D Heer, et al.

Animal microbiome

Genetic and metabolic links between the murine microbiome and memory – Jian-Hua Mao, et al. – Microbiome

Plant root-soil microbiome

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions – Stien Beirinckx, et al. – Microbiome

Microbial interactions

Preprint: Expanding the diversity of bacterioplankton isolates and modeling isolation efficacy with large scale dilution-to-extinction cultivation – Michael W. Henson, et al.

 

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