February 9, 2022

Today’s digest includes a Nature Medicine news feature on the role of preprints in the COVID-19 pandemic. Also included are an article about unsupervised clustering methods for microbiome data, the response of anammox consortia to nutrient starvation, and a handful of interesting preprints.

Animal experiments

Preprint: Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig – Gaio et al. – bioRxiv

Plant, root, and soil microbiome

Preprint: Ecological insights into soil health according to the life-history traits and environment-wide associations of bacteria in agricultural soils – Wilhelm et al. – bioRxiv

Water and extremophile microbiome

Response and resilience of anammox consortia to nutrient starvation – Wang et al. – Microbiome

Bioinformatics

Preprint: Model-free prediction of microbiome compositions – Asher & Bashan – bioRxiv

Preprint: Predicting the re-distribution of antibiotic molecules caused by inter-species interactions in microbial communities – Reding – bioRxiv

Performance determinants of unsupervised clustering methods for microbiome data – Shi et al. – Microbiome

Science, publishing, and career

Rise of the preprint: how rapid data sharing during COVID-19 has changed science forever – Watson – Nature Medicine

December 20, 2021

Today’s digest is a grab bag that includes research articles on the vaginal microbiota, the gut microbiota of dairy calves, microbial loads in medical waste, and more! I’ve also highlighted a non-microbiology article that found that pet dog owners were significantly less depressed than non-pet owners during the pandemic. So if you’re looking for more reasons to adopt a new furry friend, you can add this one to the list!

General microbiome

Genomic comparison and phenotypic profiling of small colony variants of Burkholderia pseudomallei – Zulkefli et al. – PLOS One

Human vaginal microbiome

Vaginal microbiota of American Indian women and associations with measures of psychosocial stress – Borgogna et al. – PLOS One

Human gut microbiome

Gut microbiota features associated with Clostridioides difficile colonization in dairy calves – Redding et al. – PLOS One

Animal microbiome

Culicoides Latreille (Diptera: Ceratopogonidae) as potential vectors for Leishmania martiniquensis and Trypanosoma sp. in northern Thailand – Sunantaraporn et al. – PLOS Neglected Tropical Diseases

Migratory wild birds carrying multidrug-resistant Escherichia coli as potential transmitters of antimicrobial resistance in China – Yuan et al. – PLOS One

Plant, root, and soil microbiome

Characterization of soils conducive and non-conducive to Prunus replant disease – Khan et al. – Plos One

Built environment

Disposal habits and microbial load of solid medical waste in sub-district healthcare facilities and households in Yilo-Krobo municipality, Ghana – Egbenyah et al. – PLOS One

Phages and viruses

A systematic review and meta-analysis of the potential non-human animal reservoirs and arthropod vectors of the Mayaro virus – Celone et al. – PLOS Neglected Tropical Diseases

Bioinformatics

Genomic prediction using low-coverage portable Nanopore sequencing – Lamb et al. – PLOS One

Development of an efficient Sanger sequencing-based assay for detecting SARS-CoV-2 spike mutations – Lim et al. – PLOS One

Kara’s non-microbiology pick

***Depression, anxiety, and happiness in dog owners and potential dog owners during the COVID-19 pandemic in the United States – Martin et al. – PLOS One

October 22, 2021

Happy Friday!

Today’s digest includes an article on the role of age in the human intestinal microbiome, research on the role of a novel Acidobacteriota in seafloor sulfur cycling, work demonstrating the use of machine learning to predict camplyobacter source data, and much more! I also included the link to a page on “The Secret World Inside You”, a science exhibit focused on the human microbiome that is at the Witte Museum in San Antonio, Texas from now until April 10, 2022. If anyone ends up checking it out, I’d love to hear about it!

Events

A microbiome science exhibit, “The Secret World Inside You,” is at The Witte Museum in San Antonio, Texas from October 16, 2021 to April 10, 2022 .

Human gut microbiome

Bile acid-independent protection against Clostridioides difficile infection – Aguirre et al. – PLOS PATHOGENS

The importance of age in compositional and functional profiling of the human intestinal microbiome – Herzog et al. – PLOS ONE

Plant, root, and soil microbiome

The chosen fewβ€”variations in common and rare soil bacteria across biomes – Bickel & Or – The ISME Journal

The fungus Kalmusia longispora is able to cause vascular necrosis on Vitis vinifera – KarΓ‘csony et al. – PLOS ONE

Water and extremophile microbiome

Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling – Flieder et al. – The ISME Journal

Beach sand oil spills select for generalist microbial populations – Heritier-Robbins et al. – The ISME Journal

Preprint: Influence of DNA extraction kits on the fungal DNA metabarcoding for freshwater environmental DNA – Matsuoka et al. – bioRxiv

Marine signature taxa and core microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake – Reboul et al. – The ISME Journal

Phages and viruses

Review: Community context matters for bacteria-phage ecology and evolution – Blazanin & Turner – The ISME Journal

Bioinformatics

Machine learning to predict the source of campylobacteriosis using whole genome data – Arning et al. – PLOS GENETICS

October 8, 2021

Today’s digest features a metagenomic meta-study on faecal microbiota transplantation, RibDif for count and compare 16S rRNA genes within a genus, and more. Also, there is a new FEMS Microbiology Letters collection of articles highlighting the evolution of education during the COVID-19 pandemic.

There is still time to join in the second 🌎 Microbiome Virtual International Forum 🌏. Recordings from previous MVIF can be found here.

And, the #Microber2021 just started! Check out this microbe edition of #Inktober drawing challenge – during October, every day a new scientific art on microbiology topic.


Global microbiome

Cultivating Healthy Connections: Exploring and Engineering the Microbial Flow That Shapes Microbiomes – Travis J. Wiles – mSystems

Neonatal microbiome

Presence of distinctive microbiome in the first-pass meconium of newborn infants – Jenni Turunen – Scientific Reports

Respiratory microbiome

Divergence of bacterial communities in the lower airways of CF patients in early childhood – John B. O’Connor – PlosOne

Gut microbiome

Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation – Thomas Schmidt – bioRxiv

Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth–gut axis – Vishnu Prasoodanan P. K. – npj Biofilms and Microbiomes

Animal microbiome

Phylogenetic systematics of Butyrivibrio and Pseudobutyrivibrio genomes illustrate vast taxonomic diversity, open genomes and an abundance of carbohydrate-active enzyme family isoforms – Sara E. Pidcock – Microbial Genomics

Animal experiment

Metabolic modulation of tumours with engineered bacteria for immunotherapy – Fernando P. Canale – Nature

Citrobacter amalonaticus Inhibits the Growth of Citrobacter rodentium in the Gut Lumen – Caroline Mullineaux-Sanders – mBio

Regulation of blood–brain barrier integrity by microbiome-associated methylamines and cognition by trimethylamine N-oxide – Lesley Hoyles – bioRxiv

Effects of prebiotic oligofructose-enriched inulin on gut-derived uremic toxins and disease progression in rats with adenine-induced chronic kidney disease – Ebru Melekoglu – PlosOne

Plant microbiome

Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria – Claudia Sanchis-LΓ³pez – mSystems

Food

Bacteriocinogenic lactic acid bacteria in the traditional cereal-based beverage Boza: a genomic and functional approach – Luciano Lopes Queiroz – bioRxiv

Bioinformatics

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes – Francisco Zorrilla – Nucleic Acids Research

RibDif: can individual species be differentiated by 16S sequencing? – Mikael Lenz Strube – Bioinformatics Advances

eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale – Carlos P Cantalapiedra – Molecular Biology and Evolution

Sequencing DNA with nanopores: Troubles and biases – Clara Delahaye and Jacques Nicolas – PlosOne

Webinars &c

Conference: Microbiome Virtual International Conference #MVIF – October 14 (Pacific Live)/15 (Atlantic Reply)

Webinar: EMBARK Fall Webinars – a webinar series focused on AMR research

Microscopy Live! – Geology – an hour of live electron microscopy, guided by the audience – Plymouth Electron Microscopy Centre (October 29)

For more, check out a collection of microbiome events HERE!


Happy #Microber2021, sci-art October!

July 16, 2021

Today’s digest features studies on environmental contamination of carbapenem-resistant Klebsiella pneumoniae in China (spoiler: extensive contamination, but has negligible impact on patient colonisation), the dynamic change and correlation of microbiome from different body sites to the treatment response as well as immune-related adverse events of immunotherapy in lung cancer patients, and more.

Also, check out a regularly-updated collection of FREE, ONLINE microbiome events. Happy Friday!

Human microbiome

*Prospective correlation between the patient microbiome with response to and development of immune-mediated adverse effects to immunotherapy in lung cancer – Justin Chau – BMC Cancer

Gut microbiome

Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner – Emmanuel Montassier – Nature Microbiology

Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects – Sandeep Verma – PlosOne

Differences in the individual curative effect of acupuncture for obese women with polycystic ovary syndrome based on metagenomic analysis: study protocol for a randomized controlled trial – Huaying Fan – Trials

Comparative Analysis of 16S rRNA Gene and Metagenome Sequencing in Pediatric Gut Microbiomes – Danielle Peterson – Frontiers in Microbiology

Resistome

*Spread of Carbapenem-Resistant Klebsiella pneumoniae in an Intensive Care Unit: A Whole-Genome Sequence-Based Prospective Observational Study – Li Wei – Microbiology Spectrum

*Linezolid- and multidrug-resistant enterococci in raw commercial dog food, Europe, 2019–2020 – Ana R. Freitas – Emerging Infectious Diseases

Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study – Huan Chen – PeerJ

Predicting antibiotic resistance gene abundance in activated sludge using shotgun metagenomics and machine learning – Yuepeng Sun – Water Research

Animal microbiome

Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers – DΓ©borah Romaskevis Gomes Lopes – Journal of Animal Science and Biotechnology

Animal experiment

An osmotic laxative renders mice susceptible to prolonged Clostridioides difficile colonization and hinders clearance – Sarah Tomkovich – bioRxiv

Bioinformatics

Critical Assessment of Metagenome Interpretation – the second round of challenges – F. Meyer – bioRxiv

Disentangling environmental effects in microbial association networks – Maria Deutschmann – bioRxiv

Webinars &c

Microbiome Virtual International Conference #MVIF – September 14

June 4, 2021

Greetings from Pittsburgh!

Today’s digest includes a review about the digestibility of adult dog diets, several articles about the human gut microbiome, an article about the spinach phyllosphere, and research about the effect of fertilizer and continuous garlic cultivation on the soil microbiome. It also includes topics such as microorganisms in ancient Siberian permafrost, the use of a probiotic consortium as an alternative to chemical remediation of oil spills, and much more!

If you want a lighter read, I’ve also included a fun Smithsonian Magazine article about the use of bacteria in art restoration.

Happy Friday!

General microbiome

Review: An evolving view on biogeochemical cycling of iron – Kappler et al. – Nature Reviews Microbiology

Review: Beyond horizontal gene transfer: the role of plasmids in bacterial evolution – RodrΓ­guez-BeltrΓ‘n et al. – Nature Reviews Microbiology

Review: Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle – Salje – Nature Reviews Microbiology

Reviews: Microbial volatile organic compounds in intra-kingdom and inter-kingdom interactions – Weisskopf et al. – Nature Reviews Microbiology

Human skin microbiome

Apple cider vinegar soaks do not alter the skin bacterial microbiome in atopic dermatitis – Luu et al. – PLOS One

Human gut microbiome

Metabolomic profiling identifies complex lipid species and amino acid analogues associated with response to weight loss interventions – Bihlmeyer et al. – PLOS One

Gut microbiome differences among Mexican Americans with and without type 2 diabetes mellitus – Kitten et al. – PLOS One

Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank – Liu et al. – Microbiome

Gut microbiota profiles of young South Indian children: Child sex-specific relations with growth – Shivakumar et al. – PLOS One

Animal experiments

Review: Soybean meal and poultry offal meal effects on digestibility of adult dogs diets – Vanelli et al. – PLOS One

Animal microbiome

A survey of mosquito-borne and insect-specific viruses in hospitals and livestock markets in western Kenya – Chiuya et al. – PLOS One

Microbiomes of clownfish and their symbiotic host anemone converge before their first physical contact – Γ‰mie et al. – Microbiome

Characterization of oral and cloacal microbial communities in cold-stunned Kemp’s ridley sea turtles (Lepidochelys kempii) during the time course of rehabilitation – McNally et al. – PLOS One

Plant, root, and soil microbiome

Influence of seasonal changes and salinity on spinach phyllosphere bacterial functional assemblage – Ibekwe et al. – PLOS One

Comparison of bacterial and archaeal communities in two fertilizer doses and soil compartments under continuous cultivation system of garlic – Zhou et al. – PLOS One

Water and extremophile microbiome

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale – Carnevali et al. – Microbiome

Urban wastewater bacterial communities assemble into seasonal steady states – LaMartina et al. – Microbiome

Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost – Liang et al. – Microbiome

Genomic and immunogenic changes of Piscine novirhabdovirus (Viral Hemorrhagic Septicemia Virus) over its evolutionary history in the Laurentian Great Lakes – Niner et al. – PLOS One

Built environment

Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites – Silva et al. – Microbiome

Microbes in the news

Italian Art Restorers Used Bacteria to Clean Michelangelo Masterpieces – Davis-Marks – Smithsonian Magazine

March 12, 2021

Today’s digest is HUGE.

Read about the healthy urogenital microbiome profiling by culturomics, gutSMASH (Specialized Primary Metabolite Analysis From Anaerobic Bacteria), (sub)strains evolution in mice, and AMPSphere (a comprehensive catalog of antimicrobial peptides).

There are interesting results of a new metaanalysis of the neonatal microbiome, maternal strain inheritance, and persistence into adolescence, evaluation of the effect of long-term freezing storage temperature on fecal samples, and estimation of the bioinformatic carbon footprint using the freely available Green Algorithms calculator. Find out more about statistics & challenges in molecular microbiology (with a reproducible research appendix!).

NEWS: The Transbiome project is a community driven research program using crowdfunding and co-creation to discover the diversity of the neo-vaginal microbiome. You can support the project here.

Check out a list of awesome webinars, courses and podcasts. Happy Friday!

Gut microbiome

*A systematic analysis of metabolic pathways in the human gut microbiota – VictΓ²ria Pascal Andreu – bioRxiv

*Strain inheritance and neonatal gut microbiota development: A meta-analysis – Daniel Podlesny and W. Florian Fricke – International Journal of Medical Microbiology

Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut – Andrea R. Watson – bioRixv

Effect of fecal microbiota transplantation on neurological restoration in a spinal cord injury mouse model: involvement of brain-gut axis – Yingli Jing – Microbiome

Review: Association between antibiotics and gut microbiome dysbiosis in children: systematic review and meta-analysis – Lucy McDonnell – Gut Microbes

Review: Salmonella versus the Microbiome – Andrew W. L. Rogers – Microbiology and Molecular Biology Reviews

Respiratory microbiome

Strain-Resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis – Marija Dmitrijeva – mBio

Oral microbiome

Review: Resilience of the oral microbiome – William G. Wade – Periodontology 2000

Skin microbiome

Skin microbiota and clinical associations in Netherton sindrome – Veera SillanpÀÀ – JID Innovations

Urogenital microbiome

*Long-term stability of the urogenital microbiota of asymptomatic European women – Magdalena Ksiezarek – BMC Microbiology

Limosilactobacillus urinaemulieris sp. nov. and Limosilactobacillus portuensis sp. nov. isolated from urine of healthy women – Magdalena Ksiezarek – International Journal of Systematic and Evolutionary Microbiology

Vaginal microbiome

The structure and diversity of strain-level variation in vaginal bacteria – Brett A. Tortelli – Microbial Genomics

Obesity is associated with lower bacterial vaginosis prevalence in menopausal but not pre-menopausal women in a retrospective analysis of the Women’s Interagency HIV Study – Elizabeth Daubert – PlosOne

Bacterial biofilm formation on vaginal ring pessaries used for pelvic organ prolapse – Felicity G. Gould – International Urogynecology Journal

Animal microbiome

*Long-term storage of feces at βˆ’80 Β°C versus βˆ’20 Β°C is negligible for 16S rRNA amplicon profiling of the equine bacterial microbiome – Stefan Gavriliuc – PeerJ

Differences in the gut microbiomes of dogs and wolves: roles of antibiotics and starch – Yuting Liu – BMC Veterinary Research

An Expanded Gene Catalog of Mouse Gut Metagenomes – Jiahui Zhu – mSphere

Animal experiments

*Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice – Bahtiyar Yilmaz – Cell Host & Microbe

The gut mycobiome of healthy mice is shaped by the environment and correlates with metabolic outcomes in response to diet – Tahliyah S. Mims – Communications Biology

Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments – Hualan Liu – Cell Reports

Tea polyphenols regulate gut microbiota dysbiosis induced by antibiotic in mice – Jie Li – Food Research International

Plant microbiome

Designing a home for beneficial plant microbiomes – Chunxu Song – Current Opinion in Plant Biology

Food

Review: Polymicrobial interaction between Lactobacillus and Saccharomyces cerevisiae: coexistence-relevant mechanisms – Zhenbo Xu – Critical Reviews in Microbiology

Viruses and phages

Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities – Christian Santos-Medellin – The ISME Journal

Review: Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review – Julie Callanan – Microorganisms

Techniques

High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes – Florian Trigodet – bioRxiv

Bioinformatics

*AMPSphere: the worldwide survey of prokaryotic antimicrobial peptides – CΓ©lio Dias Santos-JΓΊnior – Zenodo

*A Statistical Perspective on the Challenges in Molecular Microbial Biology – Pratheepa Jeganathan and Susan P. Holmes – arXiv

*The carbon footprint of bioinformatics – Jason Grealey – bioRxiv

*Make Interactive Complex Heatmaps in R – Zuguang Gu and Daniel Huebschmann – bioRxiv

Machine learning applications in microbial ecology, human microbiome studies, and environmental monitoring – Ryan B.Ghannam and Stephen M.Techtmann – Computational and Structural Biotechnology Journal

Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit – Fernando Meyer – Nature Protocols

STATegra: Multi-Omics Data Integration – A Conceptual Scheme With a Bioinformatics Pipeline – Nuria Planell – Frontiers in Genetics

Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences – Grace A. Blackwell – bioRxiv

clinker & clustermap.js: automatic generation of gene cluster comparison figures – Cameron L M Gilchrist & Yit-Heng Chooi – Bioinformatics

gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models – Johannes Zimmermann – Genome Biology

Webinars

mSystems Thinking Series: Diversity, Equity, and Inclusion in Microbiology – ASM – March 26

The Microbiome Centers Consortium Seminar Series – weekly seminars featuring early career researchers – Thursdays

Americas Webinar: Mother’s Milk & Baby’s Bacteria: Discoveries from the CHILD Cohort Study – Meghan Azad – April 14

Courses & Workshops

Get R Done: R Tutorials video series – Chad C. Williams

Machine Learning in Genomics: Tools, Resources, Clinical Applications and Ethics – the NHGRI Genomic Data Science Working Group of the National Advisory Council for Human Genome Research – April 13-14

Podcast

February 2021 Pod: Global Changβ€ͺe‬ – Bengtsson-Palme Lab – Microbiology Lab Pod

Enhancers with Molly Gasperini – Jacob Schreiber – The Bioinformatics Chat

Matthew Schechter: Metagenomics History Part 1 and 2 – Leo Elworth – The Bioinformatics and Beyond Podcast

Ep. 33 Oyster Microbiome with Dr. Rachel Diner – Julie Laurin – Planet B612

Art

UMich Microbial Masterpieces – Community for microbe enthusiasts and artists – Erica Gardner, Anna Urso, Bruna Iunes Sanches
*Check out their giant Winogradsky Panel in the Duderstadt Center gallery

February 12, 2021

Today’s quite diverse digest features: the role of gut commensal fungi mycobiota in shaping the human protective IgG antibody repertoire, Mouse Microbial Genome Collection, gut microbiome – lymphocytes – diet link, competition between Gardnerella species, microbiota-derived bile acids pool as a mediator of host–microbiota interactions, multiscale variation in genome graphs, and a list of awesome webinars, courses and podcasts. Check out two cool science and art projects, Bacterial Alphabet and Microbe Crayon. Happy Friday!

Gut microbiome

*Human gut mycobiota tune immunity via CARD9-dependent induction of anti-fungal IgG antibodies – Itai Doron – Cell

*Functional and taxonomic comparison of mouse and human gut microbiotas using extensive culturing and metagenomics – Benjamin S. Beresford-Jones – bioRxiv

*High intake of vegetables is linked to lower white blood cell profile and the effect is mediated by the gut microbiome – Cristina Menni – BMC Medicine

The Reactobiome Unravels a New Paradigm in Human Gut Microbiome Metabolism – Gholamreza Bidkhori – bioRxiv

Spatial analysis of gut microbiome reveals a distinct ecological niche associated with the mucus layer – Kellyanne Duncan – Gut Microbes

Review: Diversity and dynamism of IgAβˆ’microbiota interactions – Kelsey E. Huus – Nature Reviews Immunology

Antibiotic-associated dysbiosis affects the ability of the gut microbiota to control intestinal inflammation upon fecal microbiota transplantation in experimental colitis models – Francesco Strati – Microbiome

Adherent-invasive E. coli metabolism of propanediol in Crohn’s disease regulates phagocytes to drive intestinal inflammation – Monica Viladomiu – Cell Host & Microbe

Adults with Prader–Willi syndrome exhibit a unique microbiota profile – Wendy J. Dahl – BMC Research Notes

Vaginal microbiome

*Population density affects the outcome of competition in co-cultures of Gardnerella species isolated from the human vaginal microbiome – Salahuddin Khan and Janet E. Hill – bioRxiv

Review: Lactic acid-containing products for bacterial vaginosis and their impact on the vaginal microbiota: A systematic review – Erica L. Plummer – PlosOne

Urinary microbiome

Functional and Taxonomic Dysbiosis of the Gut, Urine, and Semen Microbiomes in Male Infertility – Scott D. Lundy – European Urology

Review: The microbiome and host mucosal interactions in urinary tract diseases – Bernadette Jones-Freeman – Mucosal Immunology

Epidemiology of urinary tract infections in children: Causative bacteria and antimicrobial therapy – Yuhei Tanaka – Paediatrics International

Human milk microbiome

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

Respiratory microbiome

Review: Respiratory microbiome in mechanically ventilated patients: a narrative review – MΓ©lanie Fromentin – Intensive Care Medicine

Animal microbiome

Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes – Xuefeng Peng – Nature Microbiology

Metagenomics of antimicrobial and heavy metal resistance in the cecal microbiome of fattening pigs raised without antibiotics – Paiboon Tunsagool – Applied and Environmental Microbiology

Unravelling the Role of Rumen Microbial Communities, Genes, and Activities on Milk Fatty Acid Profile Using a Combination of Omics Approaches – Sokratis Stergiadis – Frontiers in Microbiology

Evaluation of the ocular surface mycobiota in clinically normal horses – Mary L. Walsh – PlosOne

Animal experiments

Colonization at birth with human CST IV cervicovaginal microbiota alters development and increases neonatal mortality in mice – Eldin JaΕ‘areviΔ‡ – bioRxiv

Novel gut pathobionts confound results in a widely used mouse model of human inflammatory disease – Samuel C Forster – bioRxiv

Low-dose exposure of glyphosate-based herbicides disrupt the urine metabolome and its interaction with gut microbiota – Jianzhong Hu – Scientific Reports

Microbiota control of maternal behavior regulates early postnatal growth of offspring – Yujung Michelle Lee – Science Advances

Probiotics

Minireview: Lactic acid bacteria as probiotics for the nose? – Ilke De Boeck – Microbial Biotechnology

*Lactobacillus bile salt hydrolase substrate specificity governs bacterial fitness and host colonization – Matthew H. Foley – PNAS

Probiotic nasal spray development by spray drying – Katarina Jokicevic – European Journal of Pharmaceutics and Biopharmaceutics

Water microbiome

Microbiota analysis of rural and urban surface waters and sediments in Bangladesh identifies human waste as driver of antibiotic resistance – Ross S. McInnes – bioRxiv

Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika – Patricia Q. Tran – The ISME Journal

Soil microbiome

Trace gas oxidizers are widespread and active members of soil microbial communities – Sean K. Bay – Nature Microbiology

Bacterial communities regulate temporal variations of the antibiotic resistome in soil following manure amendment – Jianhua Cheng – Environmental Science and Pollution Research

Techniques

Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method – Pascal M. Frey – mSystems

Bioinformatics

*Enabling multiscale variation analysis with genome graphs – Brice Letcher – bioRxiv

HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes – Yu Li – Microbiome

BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence – Benjamin Hepp – Bioinformatics

Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN) – Renaud Van Damme – Plos Computational Biology

PATO: Pangenome Analysis Toolkit – Miguel D. FernΓ‘ndez-de-Bobadilla – bioRxiv

Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets – Nicholas D. Youngblut and Ruth E. Ley – bioRxiv

Webinars

UCC Science Society STEMinar: The Gut Microbiome, Health & Disease. You truly are what you eat – Paul O’Toole – 15 February

SGBUG (Singapore Bacterial Ultra Group) seminar: Human Gut Bacteria, Bile Acids, and Host Physiology – Sloan Devlin – 18 February

MicroSeminars 2021 – Free Web-based Microbiology Seminar Series

Biofilm Baithak – An India-specific Meetup – India Biofilms Society- 20-27 February 2021.

Klebsiella Virtual Seminar Series 2021 #KlebClub2021 – Department of Microbiology and Immunology, University of Michigan

Courses

Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R – The Wellcome Genome Campus

Next Generation Sequencing Bioinformatics course – Wellcome Genome Campus Advanced Courses & Scientific Conferences – H3Abionet

Biobanking – Institut Pasteur

Podcasts

Season 2, Ep. 2: Building Biomes with Jack Gilbert – Ruairi Robertson – Biomes

Reverse mentoring with Martin Dougherty – Alice Matimba – Your Digital Mentor

Episode 17: Post-docs Part 2: Hiring – Stephanie Hicks and John Muschelli – The Corresponding Author

Episode 235: Green algae and fatty acids – Vincent Racaniello, Elio Schaechter, Michele Swanson, and Michael Schmidt – This week in microbiology podcast

Dr. Heer Mehta: Antibiotic Resistance and Experimental Evolution – Leo Elworth – The Bioinformatics and Beyond Podcast

Science and Art

Microbe Crayon Project – Anne A. Madden

Drawing the #BacterialAlphabet – NoΓ©mie Matthey

November 26, 2020

Greetings from Pittsburgh!

Today’s digest is heavy on environmental microbiology work, especially plant, root, and soil microbiome studies. I also want to highlight a fun research paper (and paired Wired article) on the microbiome of da Vinci’s drawings.

Happy reading! And for all of those in the U.S. who are celebrating the Thanksgiving holiday, please be safe and follow all local COVID precautions.


Multi-site human microbiome

Mycobiome changes in the vitreous of post fever retinitis patients – Arunasri et al. – PLOS ONE

Review: Metabolomics analysis of microbiota-gut-brain axis in neurodegenerative and psychiatric diseases – Konjevod et al. – Journal of Pharmaceutical and Biomedical Analysis

Animal experiments

Cerumen microbial community shifts between healthy and otitis affected dogs – Borriello et al. – PLOS ONE

Plant, root, and soil microbiome

The difference between cellulolytic β€˜culturomes’ and microbiomes inhabiting two contrasting soil types – Evdokimova et al. – PLOS ONE

Diversity of bacteria populations associated with different thallus regions of the brown alga Laminaria digitata – Ihua et al. – PLOS ONE

High nitrogen concentration alter microbial community in Allium fistulosum rhizosphere – Zhao et al. – PLOS ONE

Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale – Zhuang et al. – npj Biofilms and Microbiomes

Water and extremophile microbiome

Shifts in methanogenic archaea communities and methane dynamics along a subtropical estuarine land use gradient – Euler et al. – PLOS ONE

Built environment

**The microbiome of Leonardo da Vinci’s drawings: A bio-archive of their history – PiΓ±ar et al. – Frontiers in Microbiology

Microbes in the news

**Meet the microbes living on Da Vinci’s iconic sketches – Simon – Wired

Science, publishing, and career

Postdocs under pressure: β€˜Can I even do this any more?’ – Woolston – Nature

November 20, 2020

Today’s digest features a systematic assessment of best practices for the sequencing-based characterization of the human vaginal microbiome, studies on link between the plaque microbiome and peri-implantitis, cutimycin [a Cutibacterium acnes-produced antibiotic that affects niche competition among the human skin microbiota] and antibiotic resistance genes in shower drains, washing machines, and dishwashers. There is a new Micro Binfie Podcast episode about moving from the wet lab into the dry lab to become a bioinformatician. Also, check out a list of interesting (freely available) events. Happy reading/listening!

Oral microbiome

*Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics – Paolo Ghensi – npj Biofilms and Microbiomes

Skin microbiome

*A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles – Jan Claesen – Science Translational Medicine

Review: Staphylococcus epidermidisβ€”Skin friend or foe? – Morgan M. Brown and Alexander R. Horswill – Plos Pathogen

Gut microbiome

Preterm Infants Harbour a Rapidly Changing Mycobiota That Includes Candida Pathobionts – Stephen A. James – Journal of Fungi

Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology – Antonio Molinaro – Nature Communications

Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers – Allyson L. Byrd – Journal of experimental medicine

Workshop report: Toward the development of a human whole stool reference material for metabolomic and metagenomic gut microbiome measurements – Rupasri Mandal – Metabolomics

Minireview: Communal Living: Glycan Utilization by the Human Gut Microbiota – Jonathon A. Briggs – Environmental Microbiology

Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut – Leszek Michalak – Nature Communications

Vaginal microbiome

*Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome – Luisa W. Hugerth – mSphere

Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth – Conor Feehily – npj Biofilms and Microbiomes

Intercepting genomic variability of Gardnerella vaginalis species through comparative genomics analyses: evolutionary and ecological implications – Chiara Tarracchini – Applied and Environmental Microbiology

Engineered phage endolysin eliminates Gardnerella in bacterial vaginosis without damaging the healthy vaginal microbiome – Christine Landlinger – medRxiv

Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid – Katelyn Brandt & Rodolphe Barrangou – BMC Microbiology

Dominance network analysis of the healthy human vaginal microbiome not dominated by Lactobacillus species – Wendy Li and Zhanshan Sam Ma – Computational and Structural Biotechnology Journal

Animal microbiome

The haybiome: Characterising the viable bacterial community profile of four different hays for horses following different pre-feeding regimens – Simon Daniels – Plos One

Review: Value of Probiotics in Canine and Feline Gastroenterology – Silke Salavati Schmitz – Veterinary Clinics of North America: Small Animal Practice

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel – Marco Gerdol – Genome Biology

Technique

Phylotype-Level Characterization of Complex Lactobacilli Communities Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach – Shaktheeshwari Silvaraju – Applied and Environmental Microbiology

Metagenomics

Metagenomic assessment of the global distribution of bacteria and fungi – Mohammad Bahram – Environmental Microbiology

Bioinformatics

On the complexity of haplotyping a microbial community – Samuel M Nicholls – Bioinformatics

Challenges in Benchmarking Metagenomic Profilers – Zheng Sun – bioRxiv

Unifying the global coding sequence space enables the study of genes with unknown function across biomes – Chiara Vanni – bioRxiv

Nucleotide-resolution bacterial pan-genomics with reference graphs – Rachel M Colquhoun – bioRxiv

Efficient storage and analysis of quantitative genomics data with the Dense Depth Data Dump (D4) format and d4tools – Hao Hou – bioRxiv

An Integrated Workflow for Enhanced Taxonomic and Functional Coverage of the Mouse Faecal Metaproteome – Nicolas Nalpas – bioRxiv

The misuse of colour in science communication – Fabio Crameri – Nature Communications

Antimicrobial Resistance

*The Household Resistome: Frequency of Ξ²-Lactamases, Class 1 Integrons, and Antibiotic-Resistant Bacteria in the Domestic Environment and Their Reduction during Automated Dishwashing and Laundering – Laura Schages – Applied and Environmental Microbiology

The unintended consequences of a surge in antibiotic resistance when removing wastewater drain biofilm – Shireen M Kotay – bioRxiv

fosM, a new family of fosfomycin resistance gene identified in bacterial species isolated from human microbiota – Sami Khabthani – Antimicrobial Agents and Chemotherapy

Heme is crucial for medium-dependent metronidazole resistance in clinical isolates of C. difficile – Ilse M. Boekhoud – bioRxiv

Events

Black In Immuno Week – Black in Immuno – 22-28 November 2020
*A collective of scientists to celebrating, amplifying, and promoting the work of Black Immunologists across the globe.

Webinar: Antibiotic Resistance in the Environment – Organizer: Resistomap – Date: Tuesday, 24 November 2020

Webinar: Microbiology Webinars – FEMS – webinar recordings available

Virtual course and symposium: Harnessing Our Inner Ecology To Track and Treat Disease – Institute for Systems Biology – October 15 and 16, 2020
*all course materials/tutorials and talks are available for free on the website

Virtual Conference on Prokaryotic Small Proteins – Organizers: Todd Gray, Kai Papenfort, Gigi Storz and Joe Wade – January 12-14, 2021

Podcast

*Moving from wet to dry with Phil Ashton – Hosts: Andrew Page, Nabil-Fareed Alikhan and Lee Katz – Micro Binfie Podcast

Real-time quantitative proteomics with Devin Schweppe – Host: Jacob Schreiber – The Bioinformatics Chat

Interspecies collaborations with Mindaugas GapΕ‘evičius – Host: Aga Pokrywka – Ferment Radio

Microbiome as Organ: Researcher Colin Hill Talks Bacteria and Bacteriophages in Human Body with Colin Hill – Host: Richard Jacobs – The Finding Genius Podcast

What Does Your Microbiome Say About You? with Colin Hill – Host: Andrea Hardy – Let’s Gut Real

Colouring booklet

Microbes, diet and beyond by Microbiome Support EU project; Illustrations by Maria Pock

Boardgame

Drugs vs Bugs, a free and exciting Print’n’Play boardgame developed by CΓ©lia Souque