Category Archives: Food Microbiology

June 2, 2020

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Happy Month of June to all,
June serves as the national month for Alzheimer’s and brain awareness. So I will start today’s digest with some news articles about the same.
Further the digest covers some very fascinating research articles about how the microbiome influences transcriptional profile in Drosophila melanogaster to peripheral blood microbial signatures in COPD. Digest also features some awesome microbe related science communication articles.
Enjoy reading!!!
Have a Safe, Healthy, Happy, and Productive month ahead.

Alzheimer’s and brain awareness news posts

Alzheimer’s & Brain Awareness Month 2020 – Bankston – ASBMB Today

Could the gut microbiome be linked to autism? – Svoboda – Nature Outlook

General microbiome
*Interactions between the microbiome and mating influence the female’s transcriptional profile in Drosophila melanogaster – Delbare et al – bioRxiv

Phenotypic changes of bacteria through opportunity and global methylation leads to antibiotic resistance – Neerathilingam et al – bioRxiv

Human nearly-sterile sites
Peripheral blood microbial signatures in COPD – Morrow et al – bioRxiv

Human gut microbiome
Prebiotics and community composition influence gas production of the human gut microbiota – Yu et al – bioRxiv

Short-term High Intensity Interval Training (HIIT) Exercise Does Not Affect Gut Bacterial Community Diversity or Composition of Lean and Overweight Men -Rettedal et al – Experimental Physiology

Animal experiments
Integrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes – Clusinska et al – Communications Biology

Water and extremophile microbiome
Phylum-level Diversity of the Microbiome of the Extremophilic Basidiomycete Fungus Pisolithus Arhizus (Scop.) Rauschert: An Island of Biodiversity in a Thermal Soil Desert – Culling et al – MicrobiologyOpen

Food microbiology
Lactobacillus Rhamnosus 2016SWU.05.0601 Regulates Immune Balance in Ovalbumin-Sensitized Mice by Modulating the Immune-Related Transcription Factors Expression and Gut Microbiota – Song et al – Journal of the Science of Food and Agriculture

Techniques
Harnessing Ultrasound-Stimulated Phase Change Contrast Agents to Improve Antibiotic Efficacy Against Methicillin-Resistant Staphylococcus aureus Biofilms – Durham et al – bioRxiv

Microbiome Science communication articles
The hunt for a healthy microbiome – Eisenstein – Nature Outlook

The complex relationship between drugs and the microbiome – Savage -Nature Outlook

The Infant Gut Microbiome and Probiotics that Work – Smilowitz and Taft – The Scientist

May 27, 2020

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Good morning everybody. It was a bit calm during the last days. Today’s Microbiome Digest tries to give a nice summary of a broad range of latest microbiome related research. Enjoy it!

General microbiome

A microbiological survey of handwashing sinks in the hospital built environment reveals differences in patient room and healthcare personnel sinks – Franco et al – Scientific Reports

Multi-site human microbiome

REVIEW: Interaction between microbiota and immunity in health and disease – Zheng, Liwinski and Elinav – Cell Research

REVIEW: A Comprehensive Review on Natural Bioactive Compounds and Probiotics as Potential Therapeutics in Food Allergy Treatment – Pratap et al. – Front. Immunol.

Editorial: The intestinal microbiota in health and disease – Day, Keenan and Tannock – Journal of the Royal Society of New Zealand

Human oral microbiome

Longitudinal Study of Oral Microbiome Variation in Twins – Freire et al. – Scientific Reports

Human skin microbiome

Skin Microbiome in Atopic Dermatitis – Edslev, Agner and Andersen – Acta Dermato-venereologica

Human gut microbiome and virome

Preprint: Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation – Sims et al. – medRxiv

The intestinal virome in children with cystic fibrosis differs from healthy controls – Coffey et al. – PLOS One

The human gut microbiota and depression: widely reviewed, yet poorly understood – Simpson, Schwartz and Simmons – Journal of Affective Disorders

The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients? – Magne et al. – Nutrients

Book Chapter: Who Inhabits Our Gut? Introducing the Human Gut Microbiota – Flint – Why Gut Microbes Matter

Book Chapter: Variability and Stability of the Human Gut Microbiome – Flint – Why Gut Microbes Matter

Book Chapter: How to Analyse Microbial Communities? – Flint – Why Gut Microbes Matter

Book Chapter: Treating the Gut Microbiome as a System – Flint – Why Gut Microbes Matter

Metabolomics

REVIEW: Application of metabolomics to the study of irritable bowel syndrome – Bennet et al. – Neurogastroenterology & Motility

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse – van de Wouw et al. – Microbiology

Preprint: Physical activity shapes the intestinal microbiome and immunity of healthy mice but has no protective effects against colitis in MUC2-/- mice – Estaki et al. – bioRxiv

Synergetic responses of intestinal microbiota and epithelium to dietary inulin supplementation in pigs – He et al. – European Journal of Nutrition

Animal microbiome (for animals in the wild)

No correlation between microbiota composition and blood parameters in nesting flatback turtles (Natator depressus) – Scheelings et al. – Scientific Reports

Linking perturbations to temporal changes in diversity, stability, and compositions of neonatal calf gut microbiota: prediction of diarrhea – Ma et al. – The ISME Journal

Plant, root, and soil microbiome

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

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

16S rRNA Gene Diversity in the Salt Crust of Salar de Uyuni, Bolivia, the World’s Largest Salt Flat – Pecher et al. – Microbiol Resour Announc

Built environment (subways, indoor surfaces)

Fungal diversity and its contribution to the biodeterioration of mural paintings in two 1700-year-old tombs of China – Ma et al. – International Biodeterioration & Biodegradation

Characterizing Microbial Signatures on Sculptures and Paintings of Similar Provenance – Torralba et al. – Microbial Ecology

Food microbiology

Proteomic and Metabolomic Correlates of Healthy Dietary Patterns: The Framingham Heart Study – Walker et al. – Nutrients

Bioinformatics/Resources

ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining – Mungan et al. – Nucleic Acid Research

Draft Genome Sequence of a Novel Species of Halococcus (Strain IIIV-5B), an Endophytic Archaeon Isolated from the Leaf Tissue of Avicennia germinans – Zayas-Rivera et al. – Microbiol Resour Announc

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 – Asnicar et al. – Nature Communications

May 22, 2020

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We’ve got a decently sized digest today with a lot of environmental microbe papers, including descriptions of novel species. There is also the Cell paper (highlighted) from Peter Turnbaugh’s group on ketogenic diets and the gut microbiome, which has been getting a lot of press. For new bioinformatic and other techniques, we have a new R package to predict functional profiles in Tax4Fun2, an assessment of phylogenetic rooting methods for bacteria, and a description of fiber intervention used in undergraduate classes for active learning.

 Have a great weekend!

Events

Today is the last day of the Virtual Microbiome Summit.

Pregnancy and early life

Women’s multisite microbial modulation during pregnancy – Luiz G. Sparvoli – Microbial Pathogenesis

Multi-site human microbiome

Review: Bi-Directional Interactions Between Microbiota and Ionizing Radiation in Head and Neck and Pelvic Radiotherapy-Clinical Relevance – Nidhya Teresa Joseph – International Journal of Radiation Biology

Human oral microbiome

Defining the oral microbiome by whole-genome sequencing and resistome analysis: the complexity of the healthy picture – Elisabetta Caselli – BMC Microbiology

Human gut microbiome

Ketogenic diets alter the gut microbiome resulting in decreased intestinal Th17 cells – Qi Yan Ang – Cell

Preprint: Host genetic and environmental factors shape the human gut resistome – Caroline I. Le Roy – bioRxiv

MinION Sequencing of colorectal cancer tumour microbiomes—A comparison with amplicon-based and RNA-Sequencing – William S. Taylor – PLOS One (Originally posted to the Digest as a pre-print, now published)

Animal experiments

Broilers divergently selected for digestibility differ for their digestive microbial ecosystems – Marion Borey – PLOS One

Dietary Isomalto/Malto‐Polysaccharides Increase Fecal Bulk and Microbial Fermentation in Mice – Rima H. Mistry – Molecular Nutrition and Food Research

Longitudinal Effects of Dietary Oxidized Lipids on the Gut Microbiome and Mycobiome in Pigs – Folagbayi Arowolo – FASEB Journal

Animal microbiome

Single-cell amplicon sequencing reveals community structures and transmission trends of protist-associated bacteria in a termite host – Michael E. Stephens – PLOS One

Plant, root, and soil microbiome

Xylella fastidiosa subsp. pauca and olive produced lipids moderate the switch adhesive versus non-adhesive state and viceversa – Valeria Scala – PLOS One

Mitochondrial genome sequence of Phytophthora sansomeana and comparative analysis of Phytophthora mitochondrial genomes – Guohong Cai – PLOS One

nirS-type denitrifying bacterial communities in relation to soil physicochemical conditions and soil depths of two montane riparian meadows in North China. – Xiaoli Han – Environmental Science and Pollution Research

Tissue-Specific Dynamics in the Endophytic Bacterial Communities in Arctic Pioneer Plant Oxyria digyna – Cindy Given – Frontiers in Plant Science

Effects of Cultured Root and Soil Microbial Communities on the Disease of Nicotiana tabacum Caused by Phytophthora nicotianae – Tianbo Liu – Frontiers in Microbiology

Novel putative rhizobial species with different symbiovars nodulate Lotus creticus and their differential preference to distinctive soil properties – M Rejili – FEMS Microbiology Letters

Water, air, and extremophile microbiome

The microbiome of alpine snow algae shows a specific inter-kingdom connectivity and algae-bacteria interactions with supportive capacities – Lisa Krug – ISME Journal

Variation of near surface atmosphere microbial communities at an urban and a suburban site in Philadelphia, PA, USA – JD Stewart – Science of the Total Environment

Pilot-scale petroleum refinery wastewaters treatment systems: performance and microbial communities’ analysis – Fatma Karray – Process Safety and Environmental Protection

Adverse effects of levofloxacin and oxytetracycline on aquatic microbial communities – Zhigao Zhou – Science of the Total Environment

Application of microbial network analysis to discriminate environmental heterogeneity in Fildes Peninsula, Antarctica – Qian Liu – Marine Pollution Bulletin

Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium – HS Tee – ISME Journal

Metabolic diversity and co-occurrence of multiple Ferrovum species at an acid mine drainage site – Christen L. Grettenberger – BMC Microbiology

Halocatena pleomorpha gen. nov. sp. nov., an extremely halophilic archaeon of family Halobacteriaceae isolated from saltpan soil – Ashish Verma – IJSEM

Unveiling Cultivable and Uncultivable Halophilic Bacteria Inhabiting Marakkanam Saltpan, India and Their Potential for Biotechnological Applications – Jojy John – Geomicrobiology Journal

Flavobacterium profundi sp. nov., isolated from a deep-sea seamount – Qian Wang – IJSEM

Food microbiology

Molecular epidemiology, genetic diversity and antimicrobial resistance of Staphylococcus aureus isolated from chicken and pig carcasses, and carcass handlers – Onyinye J. Okorie-Kanu – PLOS One

Traditional milk transformation schemes in Côte d’Ivoire and their impact on the prevalence of Streptococcus bovis complex bacteria in dairy products – Aimé R Sanhoun – PLOS One

Comparison of Microbial Communities and Amino Acid Metabolites in Different Traditional Fermentation Starters Used during the Fermentation of Hong Qu Glutinous Rice Wine – Zhang-Cheng Liang – Food Research International

Preprint: Monitoring the microbiome for food safety and quality using deep shotgun sequencing – Kristen L. Beck – bioRxiv

Viruses

Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)? – Ping Liu – PLOS Pathogens

Vector competence of Aedes aegypti from New Caledonia for the four recent circulating dengue virus serotypes – Olivia O’Connor – PLOS Neglected Tropical Diseases

Bioinformatics

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences – Franziska Wemheuer – Environmental Microbiome

Techniques

Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families – Taylor Wade – PLOS One

Science education techniques: Fiber Force: A Fiber Diet Intervention in an Advanced Course-Based Undergraduate Research Experience (CURE) Course – Julia Massimelli Sewall – Journal of Microbiology & Biology Education

Science and art

This photographer creates prints with algae.

Non-microbiology picks:

Herd of fuzzy green “glacier mice” baffles scientists.

May 19, 2020

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Good afternoon from sunny South Wales!

Today’s digest has a lot of great papers, with something for just about everyone. We’ll start off with a bang, and highlight a great paper in which Rajasekaran and collegaues challenge the current dogma that human intervertebral discs are sterile using a 16S rRNA sequencing approach.

We then have an interesting, or perhaps concerning paper looking at the prevalence of underreported parasites in laboratory zebrafish populations. A must read for anybody using zebrafish models. We also have plenty of papers concerning plant and water microbiomes, including a rather huge report on ocean systems.

Finally, with the current health climate, what better paper peruse than the contribution of Qureshi et al. who have demonstrated that gender neutral bathrooms are more rapidly colonised than single gender bathrooms. If recent anecdotal news articles are to be believed (although they seldom are) it’s usually the men letting the side down. You’ve got to wash those hands!

I hope everyone is staying safe, and enjoys today’s post!

COVID-19

Preprint: Identification of five antiviral compounds from the Pandemic Response Box targeting SARS-CoV-2 – Holwerda et al.

General microbiome

Longitudinal Study of Oral Microbiome Variation in Twins – Freire et al. – Sci Rep

Human nearly-sterile sites

Human intervertebral discs harbour a unique microbiome and dysbiosis determines health and disease – Rajasekaran et al. – European Spine Journal

Human gut microbiome

Early signs of gut microbiome aging: biomarkers of inflammation, metabolism, and macromolecular damage in young adulthood – Gaydosh et al. – The Journals of Gerontology

Animal experiments

Behavioural effects of the common brain-infecting parasite Pseudoloma neurophilia in laboratory zebrafish (Danio rerio) – Midttun et al. – Sci Rep

Lactobacillus plantarum FRT10 alleviated high-fat diet–induced obesity in mice through regulating the PPARα signal pathway and gut microbiota – Cai et al. – Applied Microbial and Cell Physiology

Animal microbiome

Factors affecting the microbiome of Ixodes scapularis and Amblyomma americanum – Brinkerhoff et al. – PLoS ONE

Preprint: Distinct Microbial Assemblages Associated with Genetic Selection for High- and Low- Muscle Yield in Rainbow Trout – Walker et al.

Whole-genome sequences of an abortive Bacillus safensis strain isolated from a mare’s uterus – Little, Hillhouse and Lawhorn – Genome Sequences

Plant, root, and soil microbiome

Preprint: A fungal member of the microbial phyllosphere antagonizes infection of Arabidopsis thaliana by the oomycete pathogen Albugo laibachii via a putative secreted hydrolase – Eitzen et al.

Preprint: Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts – Higdon et al.

Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood – Gómez-Brandón et al. – Sci Rep

Fruitbody chemistry underlies the structure of endofungal bacterial communities across fungal guilds and phylogenetic groups – Pent, Bahram and Põldmaa – ISME J

Endophytic fungal community in grape is correlated to foliar age and domestication – Fan et al. – Annals of Microbiology

Water and extremophile microbiome

Microbial genomics of the global ocean system – Joye and Kostka – Coloqium Report

How do microbiota associated with an invasive seaweed vary across scales? – Bonthond et al. – Molecular Ecology

Preprint: Differences in the microbiota of native and non-indigenous gelatinous zooplankton organisms in a low saline environment – Jaspers et al.

Built environment

Gender‐neutral bathroom surfaces recolonized by microbes more quickly than single gender bathrooms – Qureshi, Kedo and Berthrong – Letters in Applied Microbiology

Food microbiology

Dynamic distribution of gut microbiota in meat rabbits at different growth stages and relationship with average daily gain (ADG) – Fang et al. – BMC Microbiology

Techniques

Preprint: Evaluation of Methods to Optimise Shotgun Metagenomic Sequencing-Based Analysis of the Microbiome of Milk – Feehily et al.

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 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 7, 2020

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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!

COVID-19

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 microbiome – EurekAlert!

Microbes on the market

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

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.