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 10, 2021

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Good morning! Today’s papers are mainly focused on the gut microbiota. A particular highlight is Li et al’s study, involving a network analysis of ulcerative colitis patient microbiotas, showing their potential role as opportunistic pathogens. Enjoy!

Gut microbiome

Iron status influences non-alcoholic fatty liver disease in obesity through the gut microbiome. Mayneris-Perxachs et al. Microbiome.

Ecological and network analyses identify four microbial species with potential significance for the diagnosis/treatment of ulcerative colitis (UC). Li et al. BMC microbiology.

A meta-analysis of Gut Microbiota in Children with Autism. Andreo-Martinéz et al. Journal of autism and developmental disorders.

Pregnancy and early life

Deviations in the gut microbiota of neonates affected by maternal group B Streptococcus colonization. Li et al. BMC microbiology.

Animal experiments

Preprint: Longitudinal changes in diet cause repeatable and largely reversible shifts in gut microbial communities of laboratory mice and are observed across segments of the entire intestinal tract. Low et al. Bioxriv.

Cage environment regulates gut microbiota independent of toll-like receptors. Lipinski et al. Infection and Immunity.

Changes of gut microbiome composition and metabolites associated with hypertensive heart failure rats. Li et al. BMC microbiology.

Plant, root and soil microbiome

Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field. Cadot et al. Microbiome.

Water and Extremophile Microbiome

Preprint: A metagenomic view of novel microbial and metabolic diversity found within the deep terrestrial biosphere. R. Osburn et al. Bioxriv.

Bioinformatics

geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response. Minot et al. Genome Biology.

May 8th, 2021

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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

May 07, 2021

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Human gut microbiome

Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome – Han et al. Microbiome

Diet, obesity, and the gut microbiome as determinants modulating metabolic outcomes in a non-human primate model – Newman et al. Microbiome

Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models – Jiang et al. mSystems

Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential – Mangalea et al. Cell Host & Microbe. 

Human respiratory microbiome

Integrative microbiomics in bronchiectasis exacerbations – Mac Aogáin et al. Nature Medicine

Probiotics

The International Scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics – Salminen et al. Nature Reviews Gastroenterology & Hepatology

Mycobiota/Fungi

Fungal taxonomy and sequence-based nomenclature – Lucking et al. Nature Microbiology

Host-Microbiota interactions

A Streptococcus Quorum Sensing System Enables Suppression of Innate Immunity – Rahbari et al. mBio

Bioinformatics

Tamock: simulation of habitat-specific benchmark data in metagenomics – Gerner et al. BMC Bioinformatics

Techniques

Whole lung tissue is the preferred sampling method for amplicon-based characterization of murine lung microbiota – Baker et al. Microbiome

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

May 4, 2021

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In today’s post – host-microbe marker for inflammatory bowel disease, evolution of soil bacterium along the climate gradient, how C. difficile exploits host metabolite under inflammatory conditions induced by its own toxins and differential response of commensals to alter C. difficle virulence.

Job Posting

Microbiome Scientific Researcher, Computational (Cancer Immunology) – Genentech South San Francisco, California

General Microbiome

Endothelium–gut communication: IGF‐1Rs crosstalk with microbiota – Zhen Bouman Chen – EMBO reports

Recent advances in marine algae oligosaccharides: structure, analysis, and potential prebiotic activities – Xu-Ting Xie – Critical Reviews in Food Science and Nutrition

Human Microbiome

Interplay between diet and gut microbiome, and circulating concentrations of trimethylamine N-oxide: findings from a longitudinal cohort of US men – Jun Li – Gut

Gut Dysbiosis Associated with Antibiotics and Disease Severity and Its Relation to Mortality in Critically Ill Patients – Masahiro Ojima – Digestive Diseases and Sciences

Effects of Totum-63 on glucose homeostasis and post-prandial glycemia: a translational study – Vivien Chavanelle – American Journal of Physiology Endocrinology and Metabolism

Impact of a fermented soy beverage supplemented with acerola by-product on the gut microbiota from lean and obese subjects using an in vitro model of the human colon – Antonio Diogo Silva Vieira – Environmental biotechnology

Decoding the matrix: multiomics reveals host-microbe biomarker for inflammatory bowel disease – Monica Viladomiu – The Journal of Clinical Investigation

Animal Microbiome

C. difficile exploits a host metabolite produced during toxin-mediated disease – Kali M. Pruss – Nature

In vivo commensal control of Clostridioides difficile virulence – Brintha P. Girinathan – BioRxiv

Description and comparison of the skin and ear canal microbiota of non-allergic and allergic German shepherd dogs using next generation sequencing – Neoklis Apostolopoulos – PlosOne

Plant, root and soil microbiome

Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient – Alexander B. Chase – PNAS

Soils and sediments host novel archaea with divergent monooxygenases implicated in ammonia oxidation – Spencer Diamond – BioRxiv

Water microbiome

Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem – Ya-Jou Chen – ISME Journal

Techniques

Comprehensive single‐PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S – Yi‐Chun Yeh – Environmental Microbiology

Bacteria

Completion of the gut microbial epi-bile acid pathway – Heidi L. Doden – Gut Microbes

Possible effects of Porphyromonas gingivalis on the blood-brain barrier in Alzheimer’s disease – Ingar Olsen – Expert Review of Anti-infective Therapy

Population genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii – Tao Luo – Nature Communications

May 3, 2021

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Water microbiome

Insights into the microbial diversity and structure in a full-scale municipal wastewater treatment plant with particular regard to Archaea – Płaza et al. – PLoS ONE

From the Andes to the desert: 16S rRNA metabarcoding characterization of aquatic bacterial communities in the Rimac river, the main source of water for Lima, Peru – Romero et al. – PLoS ONE

Distribution and diversity of eukaryotic microalgae in Kuwait waters assessed using 18S rRNA gene sequencing – Kumar et al. – PLoS ONE

Plant microbiome

Toward understanding microbiota homeostasis in the plant kingdom – Paasch & He – PLoS Pathogens

Animal microbiome

Seasonal dynamics of diet–gut microbiota interaction in adaptation of yaks to life at high altitude – Guo et al. – npj Biofilms and Microbiomes

Low biomass microbiome

Experimental parameters defining ultra-low biomass bioaerosol analysis – Luhung et al. – npj Biofilms and Microbiomes

Human gut microbiome

A rich meconium metabolome in human infants is associated with early-life gut microbiota composition and reduced allergic sensitization – Petersen et al. – Cell Reports Medicine

May 1, 2021

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Have a great International Workers’ Day! Today, in this Digest: a review article about the role of butyrate (a product of microbiome activity) in the early development of microbiota. We have also: probiotics and COVID19, microbiota toxins and cardiovascular disease, microbiome studies from Indonesia, a US cohort study investigating links between the microbiome, diet, and TMAO levels; several articles about connections between the diet and the microbiome, shrimp microbiota, and more!   

Human and General Microbiome

Review: Microbial driven genetic variation in holobionts – Ilana Zilber-Rosenberg and Eugene Rosenberg – FEMS Microbiology Reviews

Review: Butyrate: A Link between Early Life Nutrition and Gut Microbiome in the Development of Food Allergy – Margherita Di Costanzo et al., – Life (MDPI)

Review: Next-Generation Probiotics and Their Metabolites in COVID-19 – Thomas Gautier et al., – Microorganisms (MDPI)

Review: Circulating bile acids as a link between the gut microbiota and cardiovascular health: Impact of Prebiotics, probiotics and polyphenol-rich foods – R.A.G. Pushpass et al., – Nutrition Research Reviews

Review: Two Gut Microbiota-Derived Toxins Are Closely Associated with Cardiovascular Diseases: A Review – Tomoya Yamashita et al., – Toxins (MDPI)

Review: Dietary Strategies for Management of Metabolic Syndrome: Role of Gut Microbiota Metabolites – Sonia Croci et al., – Nutrients (MDPI)

Review: Challenging Cosmetic Innovation: The Skin Microbiota and Probiotics Protect the Skin from UV-Induced Damage – Djouhar Souak et al., – Microorganisms (MDPI)

Perspective: Gut microbiota through an evolutionary lens – Rachel N. Carmody et al., – Science

Gut Microbiome of Indonesian Adults Associated with Obesity and Type 2 Diabetes: A Cross-Sectional Study in an Asian City, Yogyakarta – Phatthanaphong Therdtatha et al., – Microorganisms (MDPI)

Interplay between diet and gut microbiome, and circulating concentrations of trimethylamine N-oxide: findings from a longitudinal cohort of US men – Jun Li et al., – Gut (BMJ)

Isolation and identification of a human intestinal bacterium capable of daidzein conversion – Yingyu Guo et al., – FEMS Microbiology Letters

Associations of fine particulate matter and its constituents with airway inflammation, lung function, and buccal mucosa microbiota in children – Yihan Wu et al., – Science of The Total Environment

Nutritional immunity: the impact of metals on lung immune cells and the airway microbiome during chronic respiratory disease – Claire Healy et al., – Respiratory Research (BMC)

Gut bacterial profile in Indian children of varying nutritional status: a comparative pilot study – Chandrasekhar Balasubramaniam et al., – European Journal of Nutrition

The sugar composition of the fibre in selected plant foods modulates weaning infants’ gut microbiome composition and fermentation metabolites in vitro – Shanthi G. Parkar et al., – Scientific Reports

Oral-Gut Microbiome Axis in Gastrointestinal Disease and Cancer – Se-Young Park et al., – cancers (MDPI)

Effects of Whole-Grain and Sugar Content in Infant Cereals on Gut Microbiota at Weaning: A Randomized Trial – Julio Plaza-Diaz et al., – Nutrients (MDPI)

Association between Dietary Habits and Fecal Microbiota Composition in Irritable Bowel Syndrome Patients: A Pilot Study – Annamaria Altomare et al., – Nutrients (MPDI)

Altered Composition of Microbiota in Women with Ovarian Endometrioma: Microbiome Analyses of Extracellular Vesicles in the Peritoneal Fluid – Sa-Ra Lee et al., – International Journal of Molecular Sciences

Pathogens

A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor – Jay Vornhagen et al., – PLoS Pathogens

Animal Microbiome

Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community – Quentin Lamy-Besnier et al., – Microbiology Resource Announcements

OTUs and ASVs Produce Comparable Taxonomic and Diversity from Shrimp Microbiota 16S Profiles Using Tailored Abundance Filters – Rodrigo García-López et al., – Genes (MDPI)

Plant Microbiome

Impact of pesticide/fertilizer mixtures on the rhizosphere microbial community of field-grown sugarcane – Weijuan Huang et al., – 3 Biotech 

Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts – Milada Solcova et al., – Microorganisms (MDPI)

Food Microbiome

Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing – Reid G. Griggs et al., – Frontiers in Microbiology

Other Microbes

Life in a Droplet: Microbial Ecology in Microscopic Surface Wetness – Tomer Orevi and Nadav Kashtan – Frontiers in Microbiology

Draft Genome Sequences of Various Bacterial Phyla Isolated from the International Space Station – Anna C. Simpson et al., – Microbiology Resource Announcements

April 29, 2021

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Good morning from Los Angeles! Today’s microbiome digest includes various interesting research and review articles. Enjoy reading.

General microbiome

The Functional Significance of Bacterial Predators – Bruce A. Hungate – mBio

Anaerobic Microbial Metabolism of Dichloroacetate – Gao Chen – mBio

Review: Recipient factors in faecal microbiota transplantation: one stool does not fit all – Camille Danne – Nature Reviews Gastroenterology and Hepatology

Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition – Clarisse Marotz – mSystems

Gut microbiome

Review: Diet-Microbiota-Brain Axis in Alzheimer’s Disease – Halle J Kincaid – Annals of Nutrition and Metabolism

Review: The significance of the gut microbiome in children with functional constipation – Monika Kwiatkowska – Advances in Clinical and Experimental Medicine

Oral microbiome

Review: Focus on the cariogenic process: microbial and biochemical interactions with teeth and oral environment – G Dipalma – Journal Of Biological Regulators And Homeostatic Agents

Respiratory microbiome

Review: A scoping review of longitudinal airway microbiota studies – Tary Yin – Expert Review of Respiratory Medicine

Vaginal microbiome

Longitudinal Profiling of the Macaque Vaginal Microbiome Reveals Similarities to Diverse Human Vaginal Communities – Nicholas S. Rhoades – mSystems

Association of Vaginal Microbiota with Signs and Symptoms of the Genitourinary Syndrome of Menopause across Reproductive Stages – Michelle Shardell – The Journal of Gerontology

Probiotics

Targeted Delivery of Probiotics: Perspectives on Research and Commercialization – K.S. Yoha – Probiotics and Antimicrobial Proteins

Animal microbiome / Animal experiments

A Single Microbiome Gene Alters Murine Susceptibility to Acute Arsenic Exposure – Qian Wang – Toxicological Sciences

Lipocalin 2 modulates dendritic cell activity and shapes immunity to influenza in a microbiome dependent manner – Martin L Watzenboeck – PloS Pathogen

Macrobdella decora: Old World Leech Gut Microbial Community Structure Conserved in a New World Leech – Emily Ann McClure – Applied and Environmental Microbiology

Influence of Anacardium occidentale leaf supplementation in broiler chicken diet on performance, caecal microbiota, blood chemistry, immune status, carcass, and meat quality – K. Adeyemi – British Poultry Science

Effects of three different mannans on obesity and gut microbiota in high-fat diet-fed C57BL/6J mice – Yajian Song – Food & Function

The fecal microbiota of piglets during weaning transition and its association with piglet growth across various farm environments – Diana Luise – PLOS ONE

Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerine birds are shaped by diet and flight-associated gut modifications – Kasun H. Bodawatta – Proceedings of the Royal Society B

Perturbation of gut microbiota plays an important role in micro/nanoplastics-induced gut barrier dysfunction – Jiyan Qiao – Nanoscale

Ameliorative Effect of Dietary Tryptophan on Neurodegeneration and Inflammation in d-Galactose-Induced Aging Mice with the Potential Mechanism Relying on AMPK/SIRT1/PGC-1α Pathway and Gut Microbiota – Jia Yin – Journal of Agricultural Food Chemistry

Plant, root and soil microbiome

Soybean Root Nodule and Rhizosphere Microbiome: Distribution of Rhizobial and Nonrhizobial Endophytes – Parris Mayhood – Applied and Environmental Microbiology

Hyperlocal Variation in Soil Iron and the Rhizosphere Bacterial Community Determines Dollar Spot Development in Amenity Turfgrass – Ming-Yi Chou – Applied and Environmental Microbiology

Manure-Based Amendments Influence Surface-Associated Bacteria and Markers of Antibiotic Resistance on Radishes Grown in Soils with Different Textures – Giselle K. P. Guron – Applied and Environmental Microbiology

Water microbiome

Human‐ and Infrastructure‐associated Bacteria in Greywater – M. Nagarkar – Journal of Applied Microbiology