July 23, 2021

Happy Friday!

It’s an exciting day here because I’m packing for fieldwork! In just a few short days I’ll be sampling from a saline aquifer in Illinois. For those of you who aren’t lucky enough to be going into the field, today’s digest is packed with a wide range of articles. Topics covered include the wild spider gut microbiome, the presence of antibiotic resistance genes in an Ohio river, the mosquito virome, the plant rhizosphere, and more.

Happy reading!

Human gut microbiome

Preprint: Phenotypic and genomic diversification in complex carbohydrate degrading human gut bacteria – Pudlo et al. – bioRxiv

Animal experiments

Effect of biochanin A on the rumen microbial community of Holstein steers consuming a high fiber diet and subjected to a subacute acidosis challenge – Harlow et al. – PLOS ONE

Ear wound healing in MRL/MpJ mice is associated with gut microbiome composition and is transferable to non-healer mice via microbiome transplantation – Velasco et al. – PLOS ONE

Animal microbiome

Preprint: Increased microbial diversity and decreased prevalence of common pathogens in the gut microbiomes of wild turkeys compared to domestic turkeys – Craft et al. – bioRxiv

Interspecific variation and functional traits of the gut microbiome in spiders from the wild: The largest effort so far – Tyagi et al. – PLOS ONE

Plant, root, and soil microbiome

Preprint: Tillage intensity and plant rhizosphere selection shape bacterial-archaeal assemblage diversity and nitrogen cycling genes – Cloutier et al. – bioRxiv

Water and extremophile microbiome

Preprint: An Ohio State Scenic River Shows Elevated Antibiotic Resistance Genes, Including Acinetobacter Tetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent – Murphy – bioRxiv

Biogeochemistry of the Antrim Shale Natural Gas Reservoir – Stemple et al. – ACS Earth and Space Chemistry

Built environment

Preprint: Novel municipal sewage-associated bacterial genomes and their potential in source tracking – Linder et al. – bioRxiv

Preprint: Structure of bacterial communities in Japanese-style bathrooms: Comparative sequencing of bacteria in shower water and showerhead biofilms using a portable nanopore sequencer – Fujiyoshi et al. – bioRxiv

Phages and viruses

Preprint: Dynamic surveillance of mosquitoes and their viromes in Wuhan during 2020 – Ren et al. – bioRxiv

Techniques

Simple mapping-based quantification of a mock microbial community using total RNA-seq data – Moriya – PLOS ONE

Preprint: Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota – Shibata et al. – bioRxiv

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 – Déborah 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

July 2nd, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a selection of interesting gut microbiome papers and preprints. In particular, Beller et al. looked at the succession of microbial communities in the infant gut from birth to 1 year of age. This digest also contains some very interesting works on environmental microbiome, as an example, Wasmund et al. investigated bacterial taxa able to degrade extracellular DNA in marine sediments.

For those interesting in bioinformatic tools and methods, this digest also contains the description of novel data ressources and tools. In particular, Pellow et al. present a new tool, SCAPP, allowing for a better assembly of plasmids from metagenomes.

Finally, today’s non-microbiology pick is a paper looking critically at the open source citation advantage effect (the hypothesis that articles made available open access may benefit from an increased number of citation) by conducting a meta-analysis of previous studies.

Have a great Weekend!


Multi-site human microbiome

Review: The human microbiome and COVID-19: A systematic review – Yamamoto et al. – Plos One

Human gut microbiome

The gut microbiome and type 2 diabetes status in the Multiethnic Cohort – Maskarinec et al. – Plos One

Preprint: Niche partitioning facilitates coexistence of closely related gut bacteria – Brochet et al. – BiorXiV

Preprint: Successional Stages in Infant Gut Microbiota Maturation – Beller et al. – BiorXiV

Fetal meconium does not have a detectable microbiota before birth – Kennedy et al. – Nature Microbiology


Animal experiments

Developmental intestinal microbiome alterations in canine fading puppy syndrome: a prospective observational study – Tal et al. – NPJ Biofilms and Microbiomes

Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance – Liu et al. – Nature Microbiology

Animal microbiome

Preprint: Enteric viruses nucleic acids distribution along the digestive tract of rhesus macaques with idiopathic chronic diarrhea – Delwart et al. – BiorXiV

Plant, root, and soil microbiome

Microbiomes of commercially-available pine nuts and sesame seeds – Fay et al. – Plos One

Spatial patterns in phage-Rhizobium coevolutionary interactions across regions of common bean domestication – Van Cauwenberghe et al. – ISME Journal

Water and extremophile microbiome

Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments – Wasmund et al. – Nature Microbiology


Phages and viruses

Preprint: High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems – Meaden et al. – BioRxiV

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome – Nayfach et al. – Nature Microbiology

Bioinformatics

SCAPP: an algorithm for improved plasmid assembly in metagenomes – Pellow et al. – Microbiome

A standardized archaeal taxonomy for the Genome Taxonomy Database – Rinke et al. – Nature Microbiology


My non-microbiology picks

Is the open access citation advantage real? A systematic review of the citation of open access and subscription-based articles – Langham-Putrow et al. – Plos One

June 25, 2021

This week, the microbial sciences community worldwide (virtually) united at the World Microbe Forum – meeting highlights you can find here #WorldMicrobeForum.

Today’s digest features studies on group B Streptococcus pathogenesis, dental microbiota and aGVHD Risk, a book about writing and publishing papers, and more. Also, check out a collection of FREE, ONLINE microbiome events. Happy Friday!


Read about the experiences of 338 early career researchers from 36 countries with their mentors in Mentorship in life sciences: voices of mentees by A. Murat Eren (Meren)!


General microbiome

Behind the paper: Describing and naming bacteria in the 21st century – Thomas Hitch – Nature blog

Hierarchical control of microbial community assembly – Sammy Pontrelli – bioRxiv

Resistome

*L-form switching confers antibiotic, phage and stress tolerance in pathogenic Escherichia coli – Aleksandra Petrovic Fabijan – bioRxiv

Gut microbiome

A newly identified protein from Akkermansia muciniphila stimulates GLP-1 secretion – Patrice D. Cani and Claude Knauf – Cell Metabolism

Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics – Anna Pryszlak – arXiv

Dispersal strategies shape persistence and evolution of human gut bacteria – Falk Hildebrand – Cell Host & Microbe

Urinary microbiome

Review: Urinary Microbiome: Yin and Yang of the Urinary Tract – Virginia Perez-Carrasco – Frontiers in Cellular and Infection Microbiology

Vaginal microbiome

Cysteine dependence in Lactobacillus iners constitutes a novel therapeutic target to modify the vaginal microbiota – Seth M. Bloom – bioRxiv

*A type VII secretion system in Group B Streptococcus mediates cytotoxicity and virulence – Brady L Spencer – bioRxiv

Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omics – Zhuye Jie – Genomics, Proteomics & Bioinformatics

Predictive functional analysis reveals inferred features unique to cervicovaginal microbiota of African women with bacterial vaginosis and high-risk human papillomavirus infection – Harris Onywera – PlosOne

Effect of metronidazole on vaginal microbiota associated with asymptomatic bacterial vaginosis – Daniel Ruiz-Perez – Access Microbiology

Oral microbiome

*Dental Biofilm Microbiota Dysbiosis Is Associated With the Risk of Acute Graft-Versus-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation – Vitor Heidrich – Frontiers in Immunology

Fusobacterium nucleatum metabolically integrates commensals and pathogens in oral biofilms – Akito Sakanaka – bioRxiv

Animal microbiome

*Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches – Sharon A. Huws – Microbiome

Animal experiments

A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes – Marion Darnaud – bioRxiv

Bioinformatics

GUNC: detection of chimerism and contamination in prokaryotic genomes – Askarbek Orakov – BMC Genome Biology

metaMIC: reference-free Misassembly Identification and Correction of de novo metagenomic assemblies – Senying Lai – bioRxiv

Open challenges for microbial network construction and analysis – Karoline Faust – The ISME Journal 2021

STRipy: a graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data – Andreas Halman – bioRxiv

Adapting macroecology to microbiology: using occupancy modelling to assess functional profiles across metagenomes – Angus S Hilts – bioRxiv


Webinars &c

Microbiome Virtual International Conference #MVIF – September 14

The International Conference on Group B Strep (ICGBS) – July 20-22

World Enterococcus Day – July 15 – Registration here

BiATA2021 Bioinformatics: from Algorithms to Applications – July 12–15 


LSfM Lecture Series & Workshops : “The Dark Side of Science: Misconduct in Biomedical Research” Dr. Elisabeth Bik – more info here – June 30

EMBARK Webinars – Kimberly Kline “Pathogenesis and persistence during Enterococcus faecalis biofilm-associated infection” and Sofia Forslund “High-throughput measurement of host and microbiota” – EMBARK project – June 30


Writing

Writing and Publishing Scientific Papers: A Primer for the Non-English Speaker – Gábor Lövei – OpenBook Publishers


Art

From Scientist to SciArtist – Eliza Wolfson


June 23, 2021

Happy Wednesday!

Today’s digest includes a review on the microbial transformations of human bile acids as well as research articles focused on extremophiles including Arthrobacter, Acidithiobacillus, and Atribacteria. Also included are a wide variety of preprints on topics such as CRISPR-Cas, the vaginal microbiome, immunocompetence in pigs, the evaluation of RNAlater for preserving field samples for metaproteomics, and more!

Happy reading!

General microbiome

Preprint: CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids – Pinilla-Redondo et al. – bioRxiv

Human respiratory microbiome

Indoor bacterial, fungal and viral species and functional genes in urban and rural schools in Shanxi Province, China–association with asthma, rhinitis and rhinoconjunctivitis in high school students – Fu et al. – Microbiome

Human vaginal microbiome

Preprint: Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data – France et al. – bioRxiv

Human gut microbiome

Review: Microbial transformations of human bile acids – Guzior & Quinn – Microbiome

Preprint: Targeted high-resolution taxonomic identification of Bifidobacterium longum subsp. infantis using human milk oligosaccharide metabolizing genes – Tso et al. – bioRxiv

An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants – Xie et al. – Microbiome

Animal experiments

Preprint: Leveraging host-genetics and gut microbiota to determine immunocompetence in pigs – Ramayo-Caldas et al. – bioRxiv

Joint contributions of the gut microbiota and host genetics to feed efficiency in chickens – Wen et al. – Microbiome

Animal microbiome

Holobiont nitrogen control and its potential for eutrophication resistance in an obligate photosymbiotic jellyfish – Röthig et al. – Microbiome

Plant, root, and soil microbiome

Preprint: Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments – Glass et al. – bioRxiv

Preprint: Seed microbiota revealed by a large-scale meta-analysis including 50 plant species – Simonin et al. – bioRxiv

Preprint: The activity and functions of subarctic soil microbial communities vary across vegetation types – Viitamäki et al. – bioRxiv

Water and extremophile microbiome

Preprint: Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep – Chen et al. – bioRxiv

Preprint: Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures – Li et al. – bioRxiv

Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir – Mo et al. – Microbiome

Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution – Shen et al. – Microbiome

Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs – Sriaporn et al. – Microbiome

Built environment

Preprint: Metagenome-based comparisons of decay rates and host-specificity of fecal microbial communities for improved microbial source tracking – Suttner et al. – bioRxiv

Phages and viruses

Preprint: Expanding clinical phage microbiology: Simulating phage inhalation for respiratory tract infections – Porat et al. – bioRxiv

Techniques

Ultra-accurate microbial amplicon sequencing with synthetic long reads – Callahan et al. – Microbiome

Preprint: Evaluation of RNAlater as a field-compatible preservation method for metaproteomic analyses of bacteria-animal symbioses – Jensen et al. – bioRxiv

Preprint: Predicting microbiome compositions through deep learning – Michel-Mata et al. – bioRxiv

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 – Rodríguez-Beltrán 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 – Émie 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

May 28, 2021

Good morning from New Jersey! A broad selection of papers to share with you today—highlights include several new bioinformatics papers and an examination of the effect of storage method on the composition of microbiome samples:

General microbiome

A global metagenomic map of urban microbiomes and antimicrobial resistance, David Danko et al., Cell

Ecology and molecular targets of hypermutation in the global microbiome, Simon Roux et al., Nature Communications

Human oral microbiome

A cocoa (Theobroma cacao L.) extract impairs the growth, virulence properties, and inflammatory potential of Fusobacterium nucleatum and improves oral epithelial barrier function, Amel Ben Lagha et al., PLOS ONE

Human skin microbiome

Composition of cutaneous bacterial microbiome in seborrheic dermatitis patients: A cross-sectional study, Martijn G.H. Sanders et al., PLOS ONE

Human gut microbiome

Gene-level metagenomic architectures across diseases yield high-resolution microbiome diagnostic indicators, Braden T. Tierney et al., Nature Communications

Altered faecal microbiome and metabolome in IgG4-related sclerosing cholangitis and primary sclerosing cholangitis, Qiaoyan Liu et al., Gut

Animal experiments

Gut microbiome variation modulates the effects of dietary fiber on host metabolism, Sofia M. Murga-Garrido et al., Microbiome

Real-time monitoring of ruminal microbiota reveals their roles in dairy goats during subacute ruminal acidosis, Xiaodong Chen et al., npj Biofilms and Microbiomes

Animal microbiome

The microbiome and mosquito vectorial capacity: rich potential for discovery and translation, Cintia Cansado-Utrilla et al., Microbiome

Bioinformatics

Preprint: A metabolomics pipeline enables mechanistic interrogation of the gut microbiome, Shuo Han et al., bioRxiv

Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing, Zachary D. Wallen, BMC Bioinformatics

Reads Binning Improves the Assembly of Viral Genome Sequences From Metagenomic Samples, Kai Song, Frontiers in Microbiology

Techniques

Preprint: Standard Sample Storage Conditions Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns, Casper Sahl Poulsen et al., bioRxiv

May 14, 2021

Today’s digest features Emu for microbial community profiling with expectation-maximization algorithm to generate taxonomic abundance profiles from full-length 16S rRNA reads, glycobiology of UTI, profiling canine fecal microbiome by long-read metagenomics with Nanopore sequencing, spatial-temporal assessment of drinking water microbiome in Puerto Rico, ancient microbial genomes from paleofeces (with 61 previously undescribed species), and more.

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


Today is the last day for #NSURP2021 applications:

The National Summer Undergraduate Research Project – A community-driven initiative to create rewarding remote summer research opportunities for BIPOC and Latinx undergraduate students in the microbial sciences.


Share your experience as an early career researcher with your academic mentor and take part in this important survey on mentorship!

Gut microbiome

Reconstruction of ancient microbial genomes from the human gut – Marsha C. Wibowo – Nature

Human and preclinical studies of the host–gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health – François Brial – Gut Microbiota

Oral microbiome

*Mechanical biofilm disruption causes microbial and immunological shifts in periodontitis patients – William Johnston – Scientific Reports

Vaginal microbiome

Review: The Complex Link between the Female Genital Microbiota, Genital Infections, and Inflammation – Smritee Dabee – Infection and Immunity

Urinary microbiome

*Review: The glycobiology of uropathogenic E. coli infection: the sweet and bitter role of sugars in urinary tract immunity – Federico Lupo – Immunology

The Good and the Bad: Ecological Interaction Measurements Between the Urinary Microbiota and Uropathogens – Laurens E. Zandbergen – Frontiers in Microbiology

Urinary prostaglandin E2 as a biomarker for recurrent UTI in postmenopausal women – Tahmineh Ebrahimzadeh – Life Science Alliance

Impact of Vaginal Estrogen on the Urobiome in Postmenopausal Women With Recurrent Urinary Tract Infection – Carrie E. Jung – Female Pelvic Medicine & Reconstructive Surgery

Animal microbiome

*Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces – Anna Cuscó – BMC Genomics

Perinatal exposure to tetracycline contributes to lasting developmental effects on offspring – Elizabeth M. Hill – Animal Microbiome

Drinking water microbiome

*Spatial-temporal targeted and non-targeted surveys to assess microbiological composition of drinking water in Puerto Rico following Hurricane Maria – Maria Catalina Sevillano – bioRxiv

Technique

Predicting the presence and abundance of bacterial taxa in environmental communities through flow cytometric fingerprinting – Jasmine Heyse – bioRixv

Sample preservation

Critical evaluation of faecal microbiome preservation using metagenomic analysis – Alena L. Pribyl – ISME Communications

Bioinformatics

*Emu: Species-Level Microbial Community Profiling for Full-Length Nanopore 16S Reads – Kristen D. Curry – bioRxiv

Microbiome differential abundance methods produce disturbingly different results across 38 datasets – Jacob T Nearing – bioRxiv

Improving metagenomic binning results with overlapped bins using assembly graphs – Vijini G. Mallawaarachchi – Algorithms for Molecular Biology

A method for achieving complete microbial genomes and improving bins from metagenomics data – Lauren M. Lui – Plos Computational Biology

Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions – J. Lima – Journal of Microbiological Methods

Webinars

EMBARK Spring Webinars – Heike Schmitt “International efforts for One Health surveillance of AMR (WHO Tricycle)” and Etienne Ruppé “On the use of Tricycle in EMBARK” – EMBARK project – May 19
Registration here
More info here

BISMiS Live – GCM 2.0: WDCM 10K Sequencing Project for Type Strains by Juncai Ma – Bergey’s Intl. Society for Microbial Systematics – May 15
Registration here
More info here

Women in Data Science 2021 – Perspectives in Industry and Academia – Bayer AG and de.NBI, Elixir Germany Event – 18 June

PPGSND thesis seminar: The dark side os science: misconduct in biomedical research – Elisabeth Bik – 20 May

mSystems Thinking Series – ASM

Courses

Riffomonas Project – R tutorials and more – PatricK Schloss

Machine learning in Python with scikit-learn – Inria

Introduction to Computer Science and Programming in Python – MIT

Using MOFA for integration of omics data – Ricard Argelaguet – May 25

Data Visualization: Use R, ggplot2, and the principles of graphic design to create beautiful and truthful visualizations of data – Andrew Heiss

Conferences

1st Young AMICI Symposium – Austrian Microbiome Initiative – May 25-26

Microbes, Social Equity, and Rural Health – The Microbes and Social Equity working group and The University of Maine Institute of Medicine – June 14–18

Podcast

Differential gene expression and DESeq2 with Michael Love – The Bioinformatics Chat – Roman Cheplyaka and Jacob Schreiber

The Fake Science Detectives with David Sanders and Elisabeth Bik – Follow the Science – Faye Flam

Research, networking and public perception of science with Linda J Kenney – Microbes and Us – Joseph Shuttleworth

The microbiome: Delicious food and solutions to the climate crisis with Lene Lange – Science Stories – Jens Degett

May 12, 2021

Good morning all! Today’s digest includes two articles discussing the role of the local tissue microbiome in cancer. In the first, Zhu et al. explore the relationship between the intratumor microbiome, immune cell infiltration, and patient survival in the context of melanoma. The second study by Wilkie et al. examines how lipopolysaccharide produced by the commensal breast microbiota impacts cancer growth.

Additionally, there is a paper by Radojević et al. in which the authors found an association between the fecal microbiota and immunogenicity of peripheral blood monocyte-derived dendritic cells in healthy donors; a study by Kim et al. showing that diet and microbiome derived amino acids impact gut enterocyte communication with the brain in Drosophila; and a paper by Tandon et al. investigating the impact of the reciprocal transplantation of water from the surface and bottom of lakes with different trophic states on microbial community composition and function.

Pregnancy and Early-Life
Metagenomic analysis of mother-infant gut microbiome reveals global distinct and shared microbial signatures. – Wang, S. et al., Gut Microbes.

Human Nearly-Sterile Sites
Intratumour microbiome associated with the infiltration of cytotoxic CD8+ T cells and patient survival in cutaneous melanoma. – Zhu, G. et al., European Journal of Cancer Research.

Lipopolysaccharide from the commensal microbiota of the breast enhances cancer growth: role of S100A7 and TLR4. – Wilkie, T. et al., Molecular Oncology.

Human Gut Microbiome
Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment. – Terrisse, S. et al., Cell Death & Differentiation.

Fecal microbiota composition associates with the capacity of human peripheral blood monocytes to differentiate into immunogenic dendritic cells in vitro. – Radojević, D. et al., Gut Microbes.

Substrate‐driven differences in tryptophan catabolism by gut microbiota and Aryl hydrocarbon Receptor activation. – Huang, Z. et al., Molecular Nutrition & Food Research.

Human Oral Microbiome
The evolution and changing ecology of the African hominid oral microbiome. – Fellows Yates, J.A. et al., PNAS.

Animal Experiments
Response of the microbiome-gut-brain axis in Drosophila to amino acid deficit. – Kim, B. et al., Nature.

Coadaptation between host genome and microbiome under long-term xenobiotic-induced selection. – Wang, G-H. et al., Science Advances.

Predicted Metabolic Function of the Gut Microbiota of Drosophila melanogaster. – Ankrah, N.Y.D. et al., mSystems.

Animal Microbiome
The microbiome of deep-sea fish reveals new microbial species and a sparsity of antibiotic resistance genes. – Collins, F.W.J. et al., Gut Microbes.

Insect Microbiome
Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees. – Callegari, M. et al., npj Biofilms Microbiomes.

Seasonal Dynamics of the Honey Bee Gut Microbiota in Colonies Under Subtropical Climate. – Castelli, L. et al., Microbial Ecology.

Plant, Root, and Soil Microbiome
Impact of cropping systems on the functional diversity of rhizosphere microbial communities associated with maize plant: a shotgun approach. – Fadiji, A.E. et al., Archive of Microbiology.

Water and Extremophile Microbiome
Meta-transcriptomic profiling of functional variation of freshwater microbial communities induced by an antidepressant sertraline hydrochloride. – Cui, H. et al., Science of the Total Environment.

Aquatic microbial community is partially functionally redundant: Insights from an in situ reciprocal transplant experiment. – Tandon, K. et al., Science of the Total Environment.

Towards enhancing coral heat tolerance: a “microbiome transplantation” treatment using inoculations of homogenized coral tissues. – Doering, T. et al., Microbiome.

Built Environment
The Bacterial Community Diversity of Bathroom Hot Tap Water Was Significantly Lower Than That of Cold Tap and Shower Water. – Zhang, C. et al., Frontiers in Microbiology.

Bioinformatics
A Protocol for Teaching Basic Next Generation Sequencing (NGS) Analysis Skills to Undergraduate Students Using Bash and R. – Fondi, M. & Bacci, G., Bacterial Pangenomics.

Techniques
Microdroplet-based system for culturing of environmental microorganisms using FNAP-sort. – Saito, K. et al., Scientific Reports.

May 8th, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a variety of interesting papers, in particular in bioinformatics! I recommend anyone interesting in metagenomic read classification to take a look at the benchmark study by Arizmendi Cardenas and collaborators. They compared read-based taxonomic classification tools on their capacity to handle ancient DNA sequences, characterized by a higher mutation rate and shorter sequences.

This digest also contains a very good review on the current state of the art network analysis methods for exploring interaction in complex microbial communities.

Finally, today’s non-microbiology pick is a piece exploring the current challenges and limitations for the annotation of microbiome dataset with high-quality metadata.

Have a great Weekend!


Human gut microbiome

Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease – Aldars-Garcia et al. – Microorganisms


Animal experiments

Millet-based supplement restored gut microbial diversity of acute malnourished pigs – Li et al. – PLOS One

A mixture of quebracho and chestnut tannins drives butyrate-producing bacteria populations shift in the gut microbiota of weaned piglets – Miragoli et al. – PLOS One

Animal microbiome

Dynamic changes occur in the DNA gut virome of female cynomolgus macaques during aging – Tan et al. – Microbiology Open

Virome Diversity among Mosquito Populations in a Sub-Urban Region of Marseille, France – Nebbak et al. – Viruses

Plant, root, and soil microbiome

Preprint: Mapping the microbial diversity and natural resistome of north Antarctica soils – Marcoleta et al. – BioRXiv

Community dynamics in rhizosphere microorganisms at different development stages of wheat growing in confined isolation environments – Ma et al. – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Book chapter: Bioprospecting Extreme Ecosystems Before They Vanish: The (Poorly Studied) Microbiology of Tropical Glaciers – Yarzabal – Extreme environment (CRC press)

Investigating variability in microbial community composition in replicate environmental DNA samples down lake sediment cores – Pearman et al. – PLOS One


Bioinformatics

Preprint: Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study – Arizmendi Cardenas et al. – BioRXiv

Review: Network analysis methods for studying microbial communities: A mini review – Matchado et al. – Computational and sctructural Biotechnology Journal

Improving metagenomic binning results with overlapped bins using assembly graphs – Mallawaarachchi et al. – Algorithms for molecular biology


My non-microbiology picks

Preprint: Current challenges in microbiome metadata collection – Rosenfeld et al. – BioRXiv