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 07, 2021

General microbiome

Cross-Scale Analyses of Animal and Human Gut Microbiome Assemblies from Metacommunity to Global Landscape – Ma – mSystems

Multi-site human microbiome

Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation – Ingham et al. – Microbiome

Human gut microbiome

Early melanoma invasivity correlates with gut fungal and bacterial profiles – Vitali et al. – British Journal of Dermatology

The Interplay between fasting, gut microbiota, and lipid profile – Mohammadzadeh et al. – IJCP

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

Effect of Differences in the Microbiome of Cyp17a1-Deficient Mice on Atherosclerotic Background – Künstner et al. – Cells

Telmisartan induces a specific gut microbiota signature which may mediate its antiobesity effect – Beckmann et al. – Pharmacological Research

Novel insights into the genetically obese (ob/ob) and diabetic (db/db) mice: two sides of the same coin – Suriano et al. – Microbiome

Animal microbiome (for animals in the wild)

Shades of grey: host phenotype dependent effect of urbanization on the bacterial microbiome of a wild mammal – Stothart & Newman – Animal Microbiome

Untargeted fecal metabolome analysis in obese dogs after weight loss achieved by feeding a high-fiber-high-protein diet – Bermudez Sanches et al. – Metabolomics

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

Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico – Moguel et al. – Scientific Reports

Bioinformatics

ORFograph: search for novel insecticidal protein genes in genomic and metagenomic assembly graphs – Dvorkina et al. – Microbiome

Techniques

Measuring and mitigating PCR bias in microbiota datasets – Silverman et al. PLOS Computational Biology

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 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 29, 2021

General microbiome

Biogeochemical dynamics and microbial community development under sulfate- and iron-reducing conditions based on electron shuttle amendment – TM Flynn et al. – PLOS ONE

Human skin microbiome

Composition of cutaneous bacterial microbiome in seborrheic dermatitis patients: A cross-sectional study – MGH Sanders et al. – PLOS ONE

Human gut microbiome

Host specificity of the gut microbiome – EK Mallot & KR Amato – Nature Reviews Microbiology

Animal experiments

Influence of genetic background and dietary oleic acid on gut microbiota composition in Duroc and Iberian pigs – A López-Garcí et al. – PLOS ONE

Animal microbiome

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

Plant, root, and soil microbiome

Saprotrophic fungal diversity predicts ectomycorrhizal fungal diversity along the timberline in the framework of island biogeography theory – T Yang et al. – ISME Communications

Soil microbial community responses to short-term nitrogen addition in China’s Horqin Sandy Land – N Yayi et al. – PLOS ONE

Specificity of assemblage, not fungal partner species, explains mycorrhizal partnerships of mycoheterotrophic Burmannia plants – Z Zhao et al. – The ISME Journal

Water and extremophile microbiome

Abundant and rare bacterial taxa structuring differently in sediment and water in thermokarst lakes in the Yellow River Source area, Qinghai-Tibet Plateau – Z Ren et al. – bioRxiv

Phages and viruses

Diversity, taxonomy and evolution of archaeal viruses of the class Caudoviricetes – Y Liu et al. – bioRxiv

Integrating Viral Metagenomics into an Ecological Framework – P Sommers et al. – Annual Review of Virology

Techniques

Spatial profiling of microbial communities by sequential FISH with error-robust encoding – Z Cao et al. – bioRxiv

May 17, 2021

Good morning from Pittsburgh.

Today’s digest is preprint-heavy and has quite a few articles focused on soil, plants, and agriculture. If you aren’t interested in those areas of research, we also have articles with topics spanning the 1918 pandemic to multi-donor fecal transplants to carbohydrate utilization by marine fungi.

Happy reading!

General microbiome

Fresh extension of Vibrio cholerae competence type IV pili predisposes them for motor-independent retraction – Chlebek et al. – Appl Environ Microbiol

Preprint: Coordination of gene expression with cell size enables Escherichia coli to efficiently maintain motility across conditions – Honda et al. – bioRxiv

Preprint: Archival influenza virus genomes from Europe reveal genomic and phenotypic variability during the 1918 pandemic – Patrono et al. – bioRxiv

Preprint: Fluorescent protein expression as a proxy of bacterial fitness in a high throughput assay – Schlechter et al. – bioRxiv

Preprint: Nanopore sequencing provides rapid and reliable insight into microbial profiles of Intensive Care Units – Viana de Siqueira et al. – bioRxiv

Human skin microbiome

Preprint: Anatomy promotes neutral coexistence of strains in the human skin microbiome – Conwill et al. – bioRxiv

Preprint: Gene- and genome-centric dynamics shape the diversity of oral bacterial populations – Utter et al. – bioRxiv

Human gut microbiome

Preprint: Two microbiota subtypes identified in Irritable Bowel Syndrome with distinct responses to the low-FODMAP diet – Vervier et al. – bioRxiv

Strain engraftment competition and functional augmentation in a multi-donor fecal microbiota transplantation trial for obesity – Wilson et al. – Microbiome

Plant, root, and soil microbiome

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula – Brown et al. – Microbiome

Preprint: A novel dual enrichment strategy provides soil- and digestate-competent N2O-respiring bacteria for mitigating climate forcing in agriculture – Jonassen et al. – bioRxiv

Preprint: Temporal dynamics of microbial transcription in wetted hyperarid desert soils – León-Sobrino et al. – bioRxiv

Preprint: Metagenomic sequencing for rapid identification of Xylella fastidiosa from leaf samples – Roman-reyna et al. – BioRxiv

Preprint: Pseudomonas arenae sp. nov., Pseudomonas glycinis sp. nov. and Pseudomonas harudinis sp. nov., three novel bacterial species and plant endophytes – Seaton et al. – bioRxiv

Preprint: Phage-resistant bacteria reveal a role for potassium in root colonization – Tzipilevich & Benfey – bioRxiv

Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems – Qian et al. – Microbiome

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

Potential and expression of carbohydrate utilization by marine fungi in the global ocean – Baltar et al. – Microbiome

Preprint: Syntrophic H2 production enhances the performance of primarily acetate-supplemented reactors treating sulphate contaminated solutions – Hessler 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