Category Archives: Human oral

May 17, 2021

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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

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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

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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 05, 2021

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Special Issue on Interplay of Gene Expression Regulation and Microbiome

Cells has a call for papers for a special issue about the ‘Interplay of Gene Expression Regulation and Microbiome‘. This Special Issue should serve as a platform to bring together recent advances in the understanding of the dynamic interplay between gene regulation and host-microbiome interaction.

Human oral microbiome

Anna Karenina and the subgingival microbiome associated with periodontitis – Altabtaei et al. – Microbiome

Human gut microbiome

[REVIEW]The Association Between Intestinal Bacteria and Allergic Diseases—Cause or Consequence? – Han et al. – Front. Cell. Infect. Microbiol.

[Review]Exploring the Modulatory Effects of Gut Microbiota in Anti-Cancer Therapy – Li, Deng & Chen – Front. Oncol.

[REVIEW]The interplay between Helicobacter pylori and gastrointestinal microbiota – Chen et al. Gut Microbes

Do Antibiotics Cause Obesity Through Long-term Alterations in the Gut Microbiome? A Review of Current Evidence – Vallianou et al. – Metabploism

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

Gut microbiota contributes to the development of hypertension in a genetic mouse model of systemic lupus erythematosus – de la Visitación et al. – British Journal of Pharmacology

Infant gut microbiota modulation by human milk disaccharides in humanized microbiome mice – Rubio-Del-Campo – Gut Microbes

Animal microbiome (for animals in the wild)

Description and comparison of the skin and ear canal microbiota of non-allergic and allergic German shepherd dogs using next generation sequencing – Apostolopoulos et al. PLOS One

Bioinformatics

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 – Beghini et al. – eLife

Techniques

Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements – Tourlousse et al. – Microbiome

April 07, 2021

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General microbiome

Primate phageomes are structured by superhost phylogeny and environment – Gogarten et al. – PNAS

Fungal‐induced glycolysis in macrophages promotes colon cancer by enhancing innate lymphoid cell secretion of IL‐22 – Zhu et al. – The EMBO Journal

A method for detection of SARS-CoV-2 RNA in healthy human stool: a validation study – Coryell et al. – The Lancet Microbe

The Ocular Microbiome and Microbiota and their Effects on Ocular Surface Pathophysiology and Disorders – Aragona et al. – Survey of Ophthalmology

Human oral microbiome

Multi-dimensional study of the oral microbiome, metabolite, and immunologic environment in peanut allergy – Ho et al. – Journal of Allergy and Clinical Immunology

Human skin microbiome

Temporal Variation in Staphylococcus aureus Protein A Genotypes from Nose and Skin in Atopic Dermatitis Patients – van Mierlo et al. – Dermatology

Sex‐Based Differences in Fecal Short‐Chain Fatty Acid and Gut Microbiota in Irritable Bowel Syndrome Patients – Sun et al. – Journal of Digestive Diseases

Human gut microbiome

[REVIEW]Ecological and evolutionary responses to antibiotic treatment in the human gut microbiota – Pennycook & Scanlan – FEMS Microbiology Reviews

Animal microbiome (for animals in the wild)

The Fecal and Serum Metabolomics of Giant Pandas Based on Untargeted Metabolomics – Yang et al. – Zoological Scienc

Microbes in space

Astrobiology of life on Earth – Hallsworth et al. – Environmental Microbiology
Mars’ surface is not universally biocidal – Hallsworth – Environmental Microbiology

Bioinformatics

Draft Genome Sequences and Antimicrobial Profiles of Three Staphylococcus epidermidis Strains from Neonatal Blood Samples – Afeke et al. – Microbiology Resource Announcements

CoCoNet: An Efficient Deep Learning Tool for Viral Metagenome Binning – Arisdakessian et al. – Bioinformatics

Techniques

Rank normalization empowers a t-test for microbiome differential abundance analysis while controlling for false discoveries – Davis, Huang & Wang – Briefings in Bioinformatics

Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing – Tourancheau et al. – Nature Methods

March 16, 2021

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Human gut microbiome

Strain-level functional variation in the human gut microbiota based on bacterial binding to artificial food particles – Patnode et al. Cell Host & Microbe. 

Debaryomyces is enriched in Crohn’s disease intestinal tissue and impairs healing in mice – Jain et al. Science.

Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn’s Disease – Dubinsky et al. mSystems

Human-associated microbiota suppress invading bacteria even under disruption by antibiotics – Letten et al. ISME

Early life 

Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life – Tsukuda et al. ISME

Human oral microbiome

Tonsillar Microbiota: a Cross-Sectional Study of Patients with Chronic Tonsillitis or Tonsillar Hypertrophy – Wu et al. mSystems

Animal experiments 

Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice – Yilmaz et al. Cell Host & Microbe

Bioinformatics

ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data – Deng & Delart. BMC Bioinformatics

March 12, 2021

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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 – Victòria 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 Sillanpää – 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 −80 °C versus −20 °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 – Célio Dias Santos-Júnior – 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 Chang‪e‬ – 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 25, 2021

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General microbiome
The evolution of coexistence from competition in experimental co-cultures of Escherichia coli and Saccharomyces cerevisiae – Jake N. Barber – ISME Journal

Human microbiome
Quantifying the effects of antibiotic treatment on the extracellular polymer network of antimicrobial resistant and sensitive biofilms using multiple particle tracking – Lydia C. Powell – npj Biofilms and Microbiomes

Biofilms harbour Clostridioides difficile, serving as a reservoir for recurrent infection – Charmaine Normington – npj Biofilms and Microbiomes

Gut microbiome
REVIEW: The contribution of gut bacterial metabolites in the human immune signaling pathway of non-communicable diseases – F. Hosseinkhani – Gut Microbes

The effect of acute moderate-intensity exercise on the serum and fecal metabolomes and the gut microbiota of cross-country endurance athletes – Mariangela Tabone – Scientific Reports

Oral microbiome
Candida albicans promotes tooth decay by inducing oral microbial dysbiosis – Qian Du – ISME Journal

Characterization of oral virome and microbiome revealed distinctive microbiome disruptions in paediatric patients with hand, foot and mouth disease – Si Xian Ho – npj Biofilms and Microbiomes

Skin microbiome
Characterization of the human skin resistome and identification of two microbiota cutotypes – Zhiming Li – Microbiome

Animal experiment
A gene co-association network regulating gut microbial communities in a Duroc pig population – Antonio Reverter – Microbiome

Modulating gut microbiota in a mouse model of Graves’ orbitopathy and its impact on induced disease – Sajad Moshkelgosha – Microbiome

Multi-compartment metabolomics and metagenomics reveal major hepatic and intestinal disturbances in cancer cachectic mice – Sarah A. Pötgens – Journal of Cachexia, Sarcopenia and Muscle

Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome – Congying Chen – Nature Communications

Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection – Franziska A. Stressmann – ISME Journal

Plant, root, and soil microbiome
REVIEW: From exploration to remediation: A microbial perspective for innovation in mining – Alan Levett – Earth-Science Reviews

Food microbiology
A Combined Metagenomics and Metatranscriptomics Approach to Unravel Costa Rican Cocoa Box Fermentation Processes Reveals Yet Unreported Microbial Species and Functionalities – Marko Verce – Frontiers in Microbiology

Water and extremophile microbiome
Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh – Daniel R. Leadbeater – Microbiome

Taxonomic and functional analyses of intact microbial communities thriving in extreme, astrobiology-relevant, anoxic sites – Alexandra Kristin Bashir – Microbiome

Genomic evidence for sulfur intermediates as new biogeochemical hubs in a model aquatic microbial ecosystem – Adrien Vigneron – Microbiome

REVIEW: The Seagrass Holobiont: What We Know and What We Still Need to Disclose for Its Possible Use as an Ecological Indicator – Chiara Conte – Water

Spatiotemporal variations and relationships of phosphorus, phosphomonoesterases, and bacterial communities in sediments from two Chilean rivers – Marco Camposa – Science of The Total Environment

Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy – Frank Xavier Ferrer-González – ISME Journal

Phages and virues
Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2 – Claudia Wylezich – Microbiome

Preliminary Assessment of Viral Metagenome from Cancer Tissue and Blood from Patients with Lung Adenocarcinoma – Hua‐Zhong Cai – Journal of Medical Virology

Bioinformatics
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data – Laura de Nies – Microbiome

CANTARE: finding and visualizing network-based multi-omic predictive models – Janet C. Siebert – BMC Bioinformatics

kLDM: Inferring Multiple Metagenomic Association Networks based on the Variation of Environmental Factors – Yuqing Yang – Genomics, Proteomics & Bioinformatics

Methods
REVIEW: Cross-species RNA-seq for deciphering host–microbe interactions – Alexander J. Westermann – Nature Review Genetics

A community resource for paired genomic and metabolomic data mining – Michelle A. Schorn – Nature Chemical Biology

Pre-prints
Cross-sectional analysis of the microbiota of the human gut and their direct environment (exposome) in a household cohort in northern Vietnam – Bich Vu Thi Ngoc – bioRxiv

HumGut: A comprehensive Human Gut prokaryotic genomes collection filtered by metagenome data – Pranvera Hiseni – bioRxiv

Comparative analysis of 16S rRNA gene and metagenome sequencing in pediatric gut microbiomes – Danielle Peterson – bioRxiv

Unifying the known and unknown microbial coding sequence space – Chiara Vanni – bioRxiv

February 24, 2021

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Today’s digest is about functional analyses of microbial community in anoxic sites, microbial life in billions of years old fluid inclusions, development and use of human skin commensal, expanded pig metagenome catalogue and a brilliant review on advances in RNAseq technologies to decipher host-microbiota interactions. Happy reading!

General microbiome

Taxonomic and functional analyses of intact microbial communities thriving in extreme, astrobiology-relevant, anoxic sites – Alexandra Kristin Bashir – Microbiome

Pseudomonas kielensis sp. nov. and Pseudomonas baltica sp. nov., isolated from raw milk in Germany – Stefanie Gieschler – International Journal of Systematic and Evolutionary Microbiology

Human microbiome

Development of a human skin commensal microbe for bacteriotherapy of atopic dermatitis and use in a phase 1 randomized clinical trial – Teruaki Nakatsuji – Nature Medicine

Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation – Travis T. Sims – Communications Biology

Characterization of the human skin resistome and identification of two microbiota cutotypes – Zhiming Li – Microbiome

Microbial analyses of blood spot surfaces collected from a laboratory and the bathroom of a female single-person household under different environmental conditions – Hee Sang You – FEMS Microbiology Letters

Animal microbiome

Antidepressants fluoxetine and amitriptyline induce alterations in intestinal microbiota and gut microbiome function in rats exposed to chronic unpredictable mild stress – Weijie Zhang – Translational Psychiatry

Ginsenoside Rk3 Ameliorates Obesity-Induced Colitis by Regulating of Intestinal Flora and the TLR4/NF-κB Signaling Pathway in C57BL/6 Mice – Hongwei Chen – Journal of Agricultural and Food Chemistry

Dietary anthocyanin-rich extract of açai protects from diet-induced obesity, liver steatosis, and insulin resistance with modulation of gut microbiota in mice – Haizhao Song – Nutrition

Effects of supplementing sow diets during late gestation with Pennisetum purpureum on antioxidant indices, immune parameters and faecal microbiota – Peng‐Fei Huang – veterinary Medicine and Science

Alterations in the gut microbiome and metabolic profile in rats acclimated to high environmental temperature – Yang Cao – Microbial Biotechnology

The pelvic flexure separates distinct microbial communities in the equine hindgut – Kailee J. Reed – Scientific Reports

Effects of urolithins on obesity-associated gut dysbiosis in rats fed on a high-fat diet – Abdulrasheed O. Abdulrahman – International Journal of Food Sciences and Nutrition

Functional Foods

Prebiotic Lactulose Ameliorates the Cognitive Deficit in Alzheimer’s Disease Mouse Model through Macroautophagy and Chaperone-Mediated Autophagy Pathways – Yan-Suan Lee – Journal of Agricultural and Food Chemistry

Water microbiome

Ingredients for microbial life preserved in 3.5 billion-year-old fluid inclusions – Helge Mißbach – Nature Communications

Techniques

Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome – Congying Chen – Nature Communications

Cross-species RNA-seq for deciphering host–microbe interactions – Alexander J. Westermann – Nature Reviews Genetics

Computational modeling of the gut microbiota reveals putative metabolic mechanisms of recurrent Clostridioides difficile infection – Michael A. Henson – Plos Computational Biology

An ambient-temperature storage and stabilization device performs comparably to flash-frozen collection for stool metabolomics in infants – Sivapriya Ramamoorthy – BMC Microbiology

Ecological rules for the assembly of microbiome communities – Katharine Z. Coyte – Plos Biology

February 16th, 2021

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Good afternoon from sunny Adelaide, Australia. Today’s digest highlights a range of interesting microbiome research, an article in Science modelling the future of SARS-CoV2, and a commentary in Cell on data sharing.

COVID-19

Immunological characteristics govern the transition of COVID-19 to endemicity – Lavine et al. Science.

Human gut microbiome

Can we modulate the breastfed infant gut microbiota through maternal diet? – Sindi et al. FEMS Microbiology Reviews. 

Impact of synbiotics on gut microbiota during early life: a randomized, double-blind study – Phavichitr et al. Scientific Reports

Adaptation of the small intestine to microbial enteropathogens in Zambian children with stunting – Amadi et al. Nature Microbiology

Genomic aberrations after short-term exposure to colibactin-producing E. coli transform primary colon epithelial cells – Iftekhar et al. Nature Communications

Animal experiments 

Human Milk-Fed Piglets Have a Distinct Small Intestine and Circulatory Metabolome Profile Relative to That of Milk Formula-Fed Piglets –  Rosa et al. – mSystems

Human oral microbiome

Impact of the repurposed drug thonzonium bromide on host oral-gut microbiomes – Simon-Soro et al. npj biofilms and microbiomes

Marine  microbiome 

Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort – Borchest et al. – mSystems

Phages and viruses

Balance between promiscuity and specificity in phage λ host range – Andrews and Fields – ISME

Bioinformatics

Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets – Luca et al – ISME

A “data sharing trust” model for rapid, collaborative science – Chan et al. –  Cell

A 16S rRNA Gene and Draft Genome Database for the Murine Oral Bacterial Community – Joseph et al. – mSystems