Category Archives: Animal microbiome

July 31, 2020

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Today’s digest features studies on hospital-associated bacterial communities on window components, the effect of urbanization on the vaginal microbiota of Amerindians, nitrate as a potential prebiotic for oral health, and the latest news in bioinformatics. Happy reading!

General microbiome

Microbial species interactions determine community diversity in fluctuating environments – Shota Shibasaki – bioRxiv

Review: The host-associated archaeome – Guillaume Borrel – Nature Reviews Microbiology

Oral microbiome

*Nitrate as a potential prebiotic for the oral microbiome – Bob T. Rosier – Scientific Reports

Skin microbiome

Deep skin dysbiosis in vitiligo patients: link with mitochondrial and immune changes – Hanene Bzioueche – medRxiv

Gut microbiome

Review: The microbiome: An emerging key player in aging and longevity– Minhoo Kim and Bérénice A. Benayoun – Translational Medicine of Aging

Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study – Kelsey E. Huus – Microbiome

Vaginal microbiome

*Changes in the vaginal microbiota across a gradient of urbanization – Daniela Vargas-Robles – Scientific Reports

Comparison between a novel molecular tool and conventional methods for diagnostic classification of bacterial vaginosis: is integration of the two approaches necessary for a better evaluation? – Margherita Scapaticci – New Microbiologica

Genome-wide mutagenesis identifies factors involved in Enterococcus faecalis vaginal adherence and persistence – Norhan Alhajjar – bioRxiv

Association between Vaginal Bacterial Microbiota and Vaginal Yeast Colonization – McKenna C Eastment – The Journal of Infectious Diseases

Urinary microbiome

Review: The microbiome in urological diseases – Kwang Woo Lee – Investigive and Clinical Urology

Review: FimH and Anti-Adhesive Therapeutics: A Disarming Strategy Against Uropathogens – Meysam Sarshar – Antibiotics

Characterization of urinary microbiome in patients with bladder cancer: Results from a single-institution, feasibility study – Juan Chipollini – Urologic Oncology: Seminars and Original Investigations

Animal microbiome

Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage – Jolinda Pollock – Scientific Reports

Vaginal Microbiota Changes During Estrous Cycle in Dairy Heifers – Juan J. Quereda – Frontiers in Veterinary Science

Animal experiment

The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic – Eliran Kadosh – Nature

An Enteric Pathogen Subverts Colonization Resistance by Evading Competition for Amino Acids in the Gut – Gustavo Caballero-Flores – Cell Host & Microbe

Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin – Damien J. Cabral – mSystems

Water and extremophile microbiome

Determining the primary sources of fecal pollution using microbial source tracking assays combined with land-use information in the Edwards Aquifer – Jessica Hinojosa – Water Research

Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities – Tyler J. Arbour – Frontiers in Microbiology

Food microbiome

Discovering microbiota and volatile compounds of surströmming, the traditional Swedish sour herring – Luca Belleggia – Food Microbiology

Built environment

*Viable bacterial communities on hospital window components in patient rooms – Patrick F. Horve – PeerJ

Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation – Ganesh Babu Malli Mohan – mSystems

Phages and viruses

Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone – Anastasia Tsiola – Viruses

Bioinformatics

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets – Yi Yue – BMC Bioinformatics

Untangling Species-Level Composition of Complex Bacterial Communities through a Novel Metagenomic Approach – Christian Milani – mSystems

Automated prediction and annotation of small proteins in microbial genomes– Matthew G Durrant and Ami S Bhatt – bioRxiv

Accurate and sensitive detection of microbial eukaryotes from metagenomic shotgun sequencing data – Abigail L. Lind – bioRxiv

MicrobeAnnotator: a user-friendly, comprehensive microbial genome annotation pipeline – Carlos A. Ruiz-Perez – bioRxiv

Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra – Caroline Weis – Bioinformatics

NetCoMi: Network Construction and Comparison for Microbiome Data in R – Stefanie Peschel – bioRxiv

Review: Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses – Ana Elena Pérez-Cobas – Microbial Genomics

Podcast

Machine learning for drug development with Marinka Zitnik – Jacob Schreiber – The Bioinformatics Chat

July 30, 2020

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Hello from Lübeck! This week started slowly but our todays post covers quite a range of topics with a couple of reviews about our understanding of the gut microbiome related to digestive diseases. Of particular note is a publication by Kadosh et al. (Nature 2020) linking the gut microbiome and p53 in mice. This highlights the role of the microenvironment on cancer in general.

● Human vaginal microbiome

Changes in the vaginal microbiota following antibiotic treatment for Mycoplasma genitalium, Chlamydia trachomatis and bacterial vaginosis – Ahrens et al. – Plos One

● Human gut microbiome

[REVIEW] Gut Microbiome Modulates Response to Cancer Immunotherapy – Khan et al. – Digestive Diseases and Sciences

[REVIEW] Healthy Human Gastrointestinal Microbiome: Composition and Function After a Decade of Exploration – Ruan et al. – Digestive Diseases and Sciences

[REVIEW] Microbiome and Its Role in Irritable Bowel Syndrome – Pimentel and Lembo – Digestive Diseases and Sciences

[REVIEW] Diet and Gut Microbes Act Coordinately to Enhance Programmed Cell Death and Reduce Colorectal Cancer Risk – Chapkin et al. – Digestive Diseases and Sciences

Diversity of Gut Microbiota and Bifidobacterial Community of Chinese Subjects of Different Ages and from Different Regions – Yang et al. – Microorganisms

[PREPRINT] Gut Microbiota Changes in Nonalcoholic Fatty Liver Disease and Concomitant Cardiovascular Diseases – Kurinna – bioarxiv

Lactobacillus plantarum-Mediated Regulation of Dietary Aluminum Induces Changes in the Human Gut Microbiota: an In Vitro Colonic Fermentation Study – Yu et al. – Probiotics and Antimicrobial Proteins

Troublesome friends within us: the role of gut microbiota on rheumatoid arthritis etiopathogenesis and its clinical and therapeutic relevance – Reyes-Castillo et al. – Clinical and Experimental Medicine

Duodenal Microbiota in Stunted Undernourished Children with Enteropathy – Chen et al. – The New Englang Journal of Medicine

Small molecules, big effects: microbial metabolites in intestinal immunity – Glotfelty, Wong and Levy – AJP Gastrointestinal and Liver Physiology

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

The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic – Kadosh et al. – Nature

Impact of PepT1 deletion on microbiota composition and colitis requires multiple generations – Viennois et al. – npj Biofilms and Microbiomes

● Plant, root, and soil microbiome

[REVIEW] Recent advances in the role of plant metabolites in shaping the root microbiome – Jacoby et al. – F1000

● Food microbiology

Selection of cereal-sourced lactic acid bacteria as candidate starters for the baking industry – Milanovic et al. – Plos One

The sources and transmission routes of microbial populations throughout a meat processing facility – Zwirzitz et al. – npj Biofilms and Microbiomes

● Phages and viruses

[PREPRINT] Characterization of the gut DNA and RNA viromes in a cohort of Chinese residents and visiting Pakistanis – Yan – bioarxiv

● Bioinformatics

[REVIEW] Tools for Analysis of the Microbiome – Galloway-Pena and Hanson – Digestive Diseases and Sciences

● Techniques

Microbial community dissimilarity for source tracking with application in forensic studies – Carter et al. – Plos One

● Microbes in the news

Pilot study examines facial microbiome diversity – Petrou – Dermatology Times

The 2020 Way To Treat Your Skin Is All About Bacteria, Bugs And Microbiomes – Driver – ELLE

July 23, 2020

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In today’s digest – duodenal microbiota linked to stunting in children, differential effects of germfree and antibiotic treated mouse models on social behavior, microbial metabolite receptor GPBAR and its interaction with bile acids, review article on engineering microbes to treat diseases and many more…happy reading!

General microbiome

The Microbiota-Gut-Immune-Glia (MGIG) Axis in Major Depression – Leszek Rudzki – Molecular Neurobiology

Engineering the gut microbiota to treat chronic diseases – Noura S. Dosoky – Applied Microbiology and Biotechnology

Human microbiome

Acute and chronic improvement in postprandial glucose metabolism by a diet resembling the traditional Mediterranean dietary pattern: Can SCFAs play a role? – Marilena Vitale – Clinical Nutrition

Linking the duodenal microbiota to stunting in a cohort of undernourished Bangladeshi children with enteropathy – Robert Y. Chen – New England Journal of Medicine

Enterobacterales Infection after Intestinal Dominance in Hospitalized Patients – Krishna Rao – mSphere

Differences in the gut Firmicutes to Bacteroidetes ratio across age groups in healthy Ukrainian population – Alexander Vaiserman – BMC Microbiology

Preprint- Association of gut microbiota with cerebral cortex and cerebrovascular abnormality in human mild traumatic brain injury – Lijun Bai – BioRxiv

Real-world study in infants fed an infant formula with two human milk oligosaccharides – Enriqueta Román – Nutricion Hospitalaria

Animal experiments

Gut microbiome composition differences among breeds impact feed efficiency in swine – Matteo Bergamaschi – Microbiome

Opposing effects of antibiotics and germ-free status on neuropeptide systems involved in social behaviour and pain regulation – Katerina V. A. Johnson – BMC Neuroscience

Local Necrotic Cells Trigger Systemic Immune Activation via Gut Microbiome Dysbiosis in Drosophila – Hina Kosakamoto – Cell Reports

Peanut skin extract ameliorates the symptoms of type 2 diabetes mellitus in mice by alleviating inflammation and maintaining gut microbiota homeostasis – Lan Xiang – Aging

Preprint- Community composition and development of the post-weaning piglet gut microbiome – D. Gaio – BioRxiv

Gut microbiota regulate tumor metastasis via circRNA/miRNA networks – Zhuxian Zhua – Gut Microbes

Porcine circovirus type 2 (PCV2) and Campylobacter infection induce diarrhea in piglets: Microbial dysbiosis and intestinal disorder – Gang Yang – Animal Nutrition

Plant, root and soil microbiome

Populations of the Parasitic Plant Phelipanche ramosa Influence Their Seed Microbiota – Sarah Huet – Frontiers in Plant Science

Domestication-driven changes in plant traits associated with changes in the assembly of the rhizosphere microbiota in tetraploid wheat – Aymé Spor – Scientific Reports

Water microbiome

Preprint- Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs – A. Meziti – BioRxiv

Preprint- Evaluation of the microbial community structure of potable water samples from occupied and unoccupied buildings using16S rRNA amplicon sequencing – Kimothy L. Smith – BioRxiv

Phages and Viruses

Preprint- Targeting of Mammalian Glycans Enhances Phage Predation in the Gastrointestinal Tract – Sabrina I. Green – BioRxiv

Techniques
Structural basis of GPBAR activation and bile acid recognition – Fan Yang – Nature

Microbes in News

Machine learning analysis reveals less diverse microbiome in children with type 1 diabetes – Healio

July 19, 2020

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Hello from the Sonoran Desert! In today’s digest, you’ll find find a lot of very interesting papers! For those interested in host-phages interactions, there is an amazing work from Ping and collaborators looking at phage infections dynamics in migrating bacterial populations. Interestingly, the authors suggests that phages may be able to “hitchhike” with moving bacteria.

To continue with our viral readings, you’ll also find an interesting perspective paper from Kuprovic and collaborators. In this piece, the authors attempt to reconstruct the virome associated to LUCA (Last Universal Cellular Ancestor). Amazingly, their reconstruction shows that a remarkably complex virome would have been associated to LUCA, suggesting an extensive viral evolution antedating LUCA!

Finally, today’s non-microbiology pick is a book, looking at the fascinating Cuatro Ciénegas Basin, located in México, a site that is often described as a real outdoor laboratory for astrobiology. Indeed, the Basin site contains gypsum-rich soil analogous to the Gale Crater in Mars, and the ponds contains extremely oligotrophic waters, which can be used to model ancient oceans chemistry. You’ll explore along the chapters the history, ecology, microbiology and evolution of this amazing site, to unravel the mysteries of this site absolutely unique on the planet.

Have a great Sunday!

Human respiratory microbiome

Review: Insights gained into respiratory infection pathogenesis using lung tissue metabolomics –  Bernatchez and McCall –  PLOS Pathogens

Human gut microbiome

Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse workers: A metagenome-wide cross-sectional study –  Van Gompel et al. –  Environment International

Review: The influence of the gut microbiome on obesity –  Blanco – Journal of the American Association of Nurse Practitioners

Animal microbiome (for animals in the wild)

Comparative analysis of the gut microbiota of Apis cerana in Yunnan using high-throughput sequencing. –  Luo et al. –  Archives of Microbiology

Plant, root, and soil microbiome

Higher tree diversity increases soil microbial resistance to drought. –  Gillespie et al. –  Communications Biology

Effect of land uses on soil microbial community structures among different soil depths in northeastern China. –  Ji et al. –  European Journal of soil Biology

Structural variability and niche differentiation of the rhizosphere and endosphere fungal microbiome of Casuarina equisetifolia at different ages. –  Huang et al. –  Environmental Microbiology

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

Substrate regulation leads to differential responses of microbial ammonia-oxidizing communities to ocean warming. –  Zheng et al. –  Nature communications

Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel. –  Arsenieff et al.  –  The ISME Journal

Lake characteristics influence how methanogens in littoral sediments respond to terrestrial litter inputs. –  Yakimovich et al. –  The ISME Journal

Built environment (subways, indoor surfaces)

Heavy metal concentrations in Brazilian port areas and their relationships with microorganisms: can pollution in these areas change the microbial community? –  Del Busso Zampieri et al. –  Environmental Monitoring and Assessment

Food microbiology

Material conversion, microbial community composition and metabolic functional succession during green soybean hull composting. –  Zhang et al. –  Bioresource Technology

Phages and viruses

Hitchhiking, collapse, and contingency in phage infections of migrating bacterial populations. –  Ping et al. – The ISME Journal

Review: The LUCA and its complex virome. –  Krupovic et al. –  Nature Review Microbiology

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat. –  Jarett et al. –  ISME Journal

Bioinformatics

IDMIL: an alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data. –  Rahman and Rangwala –  Bioinformatics

My non-microbiology pick

Book: Astrobiology and Cuatro Ciénegas Basin as an Analog of Early Earth. –  Medina-Chávez et al. –  Cuatro Ciénegas Basin: An Endangered Hyperdiverse Oasis. Springer

July 17, 2020

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Human microbiome

Covid-19: disinfectants and sanitisers are changing microbiomes. Ajit Singh.
BMJ.

Probiotics and COVID-19: one size does not fit all. Joyce WY Mak. The Lancet Gastroenterology & Hepatology.

Probiotics and COVID-19. Eric Giannoni. The Lancet Gastroenterology & Hepatology.

Animal microbiome
The Intestinal Microbiome Restricts Alphavirus Infection and Dissemination through a Bile Acid-Type I IFN Signaling Axis. Emma S. Winkler.Cell

Built-in environment
Bed bugs shape the indoor microbial community composition of infested homes. Madhavi L.Kakumanua. Science of the Total Environment.

Pre-print
Metagenomic analysis of the cow, sheep, reindeer and red deer rumen. Laura Glendinning. bioRxiv.

Microbial Diversity of Co-occurring Heterotrophs in Cultures of Marine Picocyanobacteria. Sean Michael Kearney. bioRxiv

Microbes in the news
The human microbiome: Everything you need to know about the 39 trillion microbes that call our bodies home. Mun-Keat Looi. ScienceFocus

July 15, 2020

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There are several notable entries in today’s digest. Registration is open for the European Learning Laboratory for the Life Sciences’ “Introducing Your Microbiome” virtual training course. The course is for European secondary school science teachers and is 5 weeks long. The 3rd Microbiome Movement will also be held this year, both virtually and in-person. Links are in the Events section.  

Today I’ve highlighted a bioinformatics paper on variant calling for cpn60 barcode sequencing and an early life paper on pre-term infant stem cell proliferation upregulated by microbial metabolites. While putting this digest together, I learned algae turns snow different colors! This is so cool to me that I’ve highlighted that paper as well. Finally, the News section includes an article for Smithsonian Magazine by Rob Dunn on quarantine’s effects on our microbial passengers.  

Happy reading!

Events

3rd Microbiome Movement – Animal Health & Nutrition Summit, taking place in North Carolina as well as digitally October 19-21, 2020.

European Learning Laboratory for the Life Sciences’ “Introducing Your Microbiome” November 2-December 7, 2020. Applications are due October 15 and the course is free.

Pregnancy and early life

Gut microbiota maturation during early human life induces enterocyte proliferation via microbial metabolites – Michael W. Dougherty – BMC Microbiology

Human gut microbiome

Perspective: Gut microbiome, big data and machine learning to promote precision medicine for cancer – Giovanni Cammarota – Nature Reviews Gastroenterology & Hepatology

Microbiome of death

Characterizing the postmortem human bone microbiome from surface-decomposed remains – Alexandra L. Emmons – PloS One

Animal experiments

Saccharomyces cerevisiae fermentation products (SCFP) stabilize the ruminal microbiota of lactating dairy cows during periods of a depressed rumen pH – Hein M. Tun – BMC Veterinary Research

Animal microbiome

A Shift Pattern of Bacterial Communities Across the Life Stages of the Citrus Red Mite, Panonychus citri – Zhen-yu Zhang – Frontiers in Microbiology

Plant, root, and soil microbiome

Nitrogen enrichment stimulates wetland plant responses whereas salt amendments alter sediment microbial communities and biogeochemical responses – Mary Donato – PloS One

Bioavailable metal (loid) s and physicochemical features co-mediating microbial communities at combined metal (loid) pollution sites – Jiawen Wang – Chemosphere

Assessing the effects of tylosin fermentation dregs as soil amendment on macrolide antibiotic resistance genes and microbial communities: Incubation study – Bo Zhang – Journal of Environmental Science and Health, Part B

Book: Phytobiomes: Current Insights and Future Vistas – Manoj Kumar Solanki – Springer

Early changes in bacterial communities in wound tissues of Pinus massoniana after inoculation with Bursaphelenchus xylophilus – Jinyan Liu – Nematology

Preprint: Unexpected diversity of CPR bacteria and nanoarchaea in the rare biosphere of rhizosphere-associated grassland soil – Alexa M. Nicolas – bioRxiv

Preprint: A Meta-analysis of the known Global Distribution and Host Range of the Ralstonia Species Complex – Tiffany Lowe-Power – bioRxiv

Water, air, and extremophile microbiome

Lipid Biomarker Record of the Serpentinite-Hosted Ecosystem of the Samail Ophiolite, Oman and Implications for the Search for Biosignatures on Mars – Sharon A Newman – Astrobiology

Metabolic acclimation of anammox consortia to decreased temperature – Tangran Huo – Environment International

Complete Genome Sequences of Two Marine Biofilm Isolates, Leisingera sp. nov. Strains 201A and 204H, Novel Representatives of the Roseobacter Group – Giselle S. Cavalcanti – Microbiology Resource Announcements

Microbial interspecific interaction and nitrogen metabolism pathway for the treatment of municipal wastewater by iron carbon based constructed wetland – Xiao Huang – Bioresource Technology

Biogeographical distribution of dissimilatory nitrate reduction to ammonium (DNRA) bacteria in wetland ecosystems around the world – Huawei Pan – Journal of Soils and Sediments

Molecular diversity of the microbial community in coloured snow from the Fildes Peninsula (King George Island, Maritime Antarctica) – Wei Luo – Polar Biology

Novel arsenic hyper-resistant bacteria from an extreme environment, Crven Dol mine, Allchar, North Macedonia – Vladimir Bermanec – Journal of Hazardous Materials

Built environment

Ozone treatment in a wind tunnel for the reduction of airborne viruses in swine buildings – Jonathan M. Vyskocil – Aerosol Science and Technology

Food microbiology

Correlation between microbial communities and key flavors during post-fermentation of Pixian broad bean paste – Ping Liu – Food Research International

Additives affect the distribution of metabolic profile, microbial communities and antibiotic resistance genes in high-moisture sweet corn kernel silage – Zhe Wu – Bioresource Technology

Shifts in autochthonous microbial diversity and volatile metabolites during the fermentation of chili pepper (Capsicum frutescens L.) – Xinxing Xu – Food Chemistry

Proteomic characterization of extracellular vesicles produced by several wine yeast species – Ana Mencher – Microbioal Biotechnology

Book Chapter: Role of Microbes for Attaining Enhanced Food Crop Production – Pankaj Sharma – Microbial Biotechnology: Basic Research and Applications

Bioinformatics

Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling – Sarah J. Vancuren – PloS One

Techniques

Preprint: Visualization of giant virus particles using BONCAT labeling and STED microscopy – Monica Berjon-Otero – bioRxiv

Microbes in the News

Human Microbiome: 39 trillion microbes and bacteria that call us home – Mun-Keat Looi – Science Focus

What Quarantine is Doing to Your Body’s Wondrous World of Bacteria – Rob Dunn – Smithsonian Magazine

July 13, 2020

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Greetings from Pittsburgh, PA!

Included is a wide range of microbial ecology articles focused on everything from the human microbiome to soil microbial fuel cells. I want to give a special highlight to the article about how the indoor microbial community changes in response to bed bug infestations. This study incorporates a few of my favorite disciplines including entomology, public health, the built environment, as well as microbiology. If you’re interested in learning more about bed bugs, I’ll also recommend one my favorite reads from a few years ago: Infested: How the bed bug infiltrated our bedrooms and took over the world by Brooke Borel.

Events and jobs

In my last microbiome digest, I gave a special plug for the National Summer Undergraduate Research Project (NSURP). NSURP is a community-driven initiative to create rewarding remote summer research opportunities for BIPOC undergraduate students in the microbial sciences. They have already paired over 140 students with summer research opportunities, but they still need mentors for remaining student applicants. Please apply and share widely!

General microbiome

The beta-diversity of Siganus fuscescens-associated microbial communities from different habitats increases with body weight – Wu et al. – Frontiers in Microbiology

Human gut microbiome

Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut – Chng et al. – Nature Ecology & Evolution

The gut microbiome during acute lifestyle transition – Devkota – Nature Medicine

Review: Challenges and emerging systems biology approaches to discover how the human gut microbiome impact host physiology – Wian and Ho – Biophysical Reviews

Animal experiments

The gut and feed residue microbiota changing during the rearing of Hermetia illucens larvae – Cifuentes et al. – Antonie van Leeuwenhoek

Animal microbiome

Effect of introduced parasites on the survival and microbiota of nestling cactus finches (Geospiza scandens) in the Galápagos Islands – Addesso et al. – Journal of Ornithology

Direct comparison of fecal and gut microbiota in the Blue Mussel (Mytilus edulis) discourages fecal sampling as a proxy for resident gut community – Griffin et al. – Microbial Ecology

Plant, root, and soil microbiome

Variable microbial communities in the non-hydrothermal sediments of the Mid-Okinawa trough – Cao et al. – Geomicrobiology Journal

Review: Microbial communities from arid environments on a global scale. A systematic review – Vásquez-Dean et al. – Biological Research

Unravelling metabolism and microbial community of a phytobed co-planted with Typha angustifolia and Ipomoea aquatica for biodegradation of doxylamine from wastewater – Xiong et al. – Journal of Hazardous Materials

Built environment

Bed bugs shape the indoor microbial community composition of infested homes – Kakumanu et al. – Science of the Total Environment

Effect of sono-thermal pre-treatment over methane production, specific activities and the microbial community of sludge anaerobic digesters – Neumann et al. – Waste and Biomass Valorization

Effects of anode materials on the performance and anode microbial community of soil microbial fuel cell – Yu et al. – Journal of Hazardous Material

Techniques

Review: Targeted microbiome depletion – Du Toit – Nature Reviews Microbiology

July 8, 2020

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Good morning! Today’s digest includes a broad selection of interesting research. Particular highlights include a study in rats that found microbiota transplantation attenuated neuroinflammation, a human study on the dramatic microbiome effects of dietary glycans, and a new technique for using drones to collect dolphin microbiome samples.

Pregnancy and early life

History of breastfeeding but not mode of delivery shapes the gut microbiome in childhood, Camille C. Cioffi et al., PLOS ONE

Preprint: Gut microbiota and fecal short-chain fatty acids are not associated with bone mass in healthy Chinese children: a cross-sectional study, Fengyan Chen et al., Research Square

Impact of Long-Term and Low-Dose Antibiotic Prophylaxis on Gut Microbiota in Children, Yuko Akagawa et al., The Journal of Urology

Human gut microbiome

Microbiome and health implications for ethnic minorities after enforced lifestyle changes, David M. Keohane et al., Nature Medicine

Preprint: Metaproteomics reveals potential signatures of disease-specific alterations in the gut microbial proteolytic events in inflammatory bowel disease, Zhixiang Yan et al., Research Square

High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans, Richard Creswell et al., Genome Medicine

Preprint: High-throughput cultivation of stable, diverse, fecal-derived microbial communities to model the intestinal microbiota, Andres Aranda-Diaz et al., bioRxiv

Preprint: pH-dependent spontaneous hydrolysis rather than gut bacterial metabolism reduces levels of the ADHD treatment, Methylphenidate, Julia Aresti et al., bioRxiv

Animal experiments

The gut microbiota attenuate neuroinflammation in manganese exposure by inhibiting cerebral NLRP3 inflammasome, Wang and Yang et al., Biomedicine & Pharmacotherapy

Magnetic fields modulate metabolism and gut microbiome in correlation with Pgc‐1α expression: Follow‐up to an in vitro magnetic mitohormetic study, Yee Kit Tai et al., The FASEB Journal

Preprint: Multi-omics analysis of aspirin treatment response in mice provide molecular insights and targets linked to liver fibrosis regression, Adil Bhat et al., bioRxiv

Animal microbiome

Limited influence of the microbiome on the transcriptional profile of female Aedes aegypti mosquitoes, Josephine Hyde et al., Scientific Reports

The gut bacterial microbiota of sea turtles differs between geographically distinct populations, T. Franciscus Scheelings et al., Endangered Species Research

Bioinformatics

Sparse reduced-rank regression for integrating omics data, Hilafu, Safo and Haine, BMC Bioinformatics

Techniques

An ecological framework to understand the efficacy of fecal microbiota transplantation, Yandong Xiao et al., Nature Communications

The use of Unmanned Aerial Vehicles (UAVs) to sample the blow microbiome of small cetaceans, Cinzia Centelleghe et al., PLOS ONE

July 4, 2020

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Greetings from Santiago, Chile! Today in this Digest, we have studies about the influence of alcohol use disorder on the microbiota, several papers about the influence of different compounds (from allicin to DAV132, a colon-targeted antibiotic adsorbent) on the microbiota. Today we have several papers about different models of plant- or soil- associated microbiomes, and a couple of papers from studies with SIV infection models. Have a nice weekend!

Human and General Microbiome

Longitudinal gut microbiome changes in alcohol use disorder are influenced by abstinence and drinking quantity – Nancy Ames et al., – Gut Microbes

Comparative evaluation of peptidome and microbiota in different types of saliva samples – Ce Zhu et al., – Annals of Translational Medicine

Preprint: Microbial control over host diet selection – Brian K Trevelline and Kevin D Kohl – BioRxiv

Functional Compounds and the Microbiome

Hemolysin BL from novel Bacillus toyonensis BV-17 induces antitumor activity both in vitro and in vivo – Jiajia Chen et al., – Gut Microbes

Modeling the effect of DAV132, a novel colon-targeted adsorbent, on fecal concentrations of moxifloxacin and gut microbiota diversity in healthy volunteers – Jinju Guk et al., – Clinical Pharmacology and Therapeutics

Allicin-induced host-gut microbe interactions improves energy homeostasis – Chuanhai Zhang et al., – The FASEB Journal

Evidence of Microbiome-Drug Interactions between the Antimalarial Lumefantrine and Gut Microbiota in Mice – Matthew M. Ippolito et al., – The American Society of Tropical Medicine and Hygiene

Contrasting effects of viscous and particulate fibers on colonic fermentation in vitro and in vivo, and their impact on intestinal water studied by MRI in a randomized trial – David Gunn et al., – The American Journal of Clinical Nutrition

Animal Microbiome / Animal Models

A theoretic approach to the mode of gut microbiome translocation in SIV-infected Asian macaques – Wendy Li and Zhanshan (Sam) Ma – FEMS Microbiology Ecology

Impact of Initial Feeding and Molting on Tachypleus tridentatus Gut Microbiota – Fengze Miao et al., – Current Microbiology 

Osmotic stress induces gut microbiota community shift in fish – Keng Po Lai et al., – Environmental Microbiology

The Gut-Eye Axis: Lessons Learned from Murine Models – Jason L. Floyd & Maria B. Grant – Ophthalmology and Therapy 

The colonic mucosa-associated microbiome in SIV infection: shift towards Bacteroidetes coincides with mucosal CD4+ T cell depletion and enterocyte damage – Kristina Allers et al., – Scientific Reports  

Plant or Soil Microbiomes

Re-Analysis of 16S Amplicon Sequencing Data Reveals Soil Microbial Population Shifts in Rice Fields under Drought Condition – Seok-Won Jang et al, – Rice 

Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations – Ryan S. McClure et al., – Scientific Reports 

Potential microbial bioindicators of phosphorus mining in a temperate deciduous forest – Laura M. Mason et al.,– Journal of Applied Microbiology

Phylogenetic signals and predictability in plant-soil feedbacks – Elizabeth M. Wandrag et al., – New Phytologist

Genomics / Bioinformatics

The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites – Feifei Xu et al., – Microbial Genomics 

LEMMI: A continuous benchmarking platform for metagenomics classifiers – Mathieu Seppey et al., – Genome Research

Other papers

Preprint: Metagenome-assembled genomes from Monte Cristo Cave (Diamantina, Brazil) reveal prokaryotic lineages as functional models for life on Mars – Amanda G Bendia et al., – BioRxiv 

Preprint: Exploring metal resistance genes and mechanisms in copper enriched metal ore metagenome – Esmaeil Forouzan Sr. et al., – BioRxiv

SARS-CoV-2 Preprints

Preprint: Alpha-1 antitrypsin inhibits SARS-CoV-2 infection – Lukas Wettstein et al., – BioRxiv

July 3rd, 2020

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General microbiome

Microbiome definition re-visited: old concepts and new challenges – Berg et al. Microbiome

Large-scale metabolic interaction network of the mouse and human gut microbiota. – Lim et al. Scientific Data

Early life microbiome

Very early-life exposure to microbiota-induced TNF drives the maturation of neonatal pre-cDC1 – Kohler et al. Gut.

Human gut microbiome

Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes – Reitmeier et al. Cell Host & Microbe

Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study – Clooney et al. Gut

Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level – Kenny et al. Cell Host & Microbe

Amending microbiota by targeting intestinal inflammation with TNF blockade attenuates development of colorectal cancer – Yang et al. Nature Cancer

Animal microbiome

A Systematic Analysis of Mosquito-Microbiome Biosynthetic Gene Clusters Reveals Antimalarial Siderophores that Reduce Mosquito Reproduction Capacity – Ganley et al. Cell Chemical Biology

Extremophile microbiome

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys – Hou et al. BMC Microbiome

Phages and viruses

Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron – Porter et al. Nature Microbiology

Bioinformatics

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data – Kieser et al. BMC Bioinformatics

Techniques

High-Throughput Stool Metaproteomics: Method and Application to Human Specimens – Gonzalez et al. mSystems

Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture – Villa et al. mSystems