Category Archives: Animal microbiome

September 7, 2022

Posted on by

General microbiome

Impact of environmental conditions and gut microbiota on the in vitro germination and growth of Clostridioides difficile – Martinez et al. – FEMS Microbiology Letters

[FORUM]Polymorphic microbes: a new emerging hallmark of cancer – Lythgoe et al. – Trends in Microbiology

A taxonomic note on the genus Prevotella: Description of four novel genera and emended description of the genera Hallella and Xylanibacter – Hitch et al. – Systematic and Applied Microbiology

A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome – Martiny et al. – PLOS Biology

Pregnancy and early life

Alterations in Vaginal Microbiota among Pregnant Women with COVID-19 – Velik et al. – Journal of Medical Virology

The Global Incidence of Adverse Events Associated with Fecal Microbiota Transplantation in Children over the Past 20 Years: A Systematic Review and Meta-Analysis – Wang et al. – Journal of Gastroenterology and Hepatology

Multi-site human microbiome

Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes – Ke, Weiss & Liu – Nature Communications

Human salivary microbiome

Salivary microbiome in chronic kidney disease: what is its connection to diabetes, hypertension, and immunity? – Liu et al. – Journal of Translational Medicine volume

Human vaginal microbiome

Does exposure to different types of menstrual protections affect the vaginal environment? – Tessandier et al. – Molecular Ecology

Human gut microbiome

High-altitude exposure decreases bone mineral density and its relationship with gut microbiota: Results from the China multi-ethnic cohort (CMEC) study – Zuo et al. – Environmental Research

Animal microbiome

Characterization of the oral and fecal microbiota associated with atopic dermatitis in dogs selected from a purebred Shiba Inu colony – Uchiyama et al. – Letters of Applied Microbiology

Probiotics or synbiotics addition to sows’ diets alters colonic microbiome composition and metabolome profiles of offspring pigs – Zhu et al. – Front. Microbiol.

Longitudinal analysis of the rectal microbiome in dogs with diabetes mellitus after initiation of insulin therapy – Laia et al. – PLOS One

Plant, root, and soil microbiome

Core Microbiota in the Rhizosphere of Heavy Metal Accumulators and Its Contribution to Plant Performance – Luo et al. – Environ. Sci. Technol.

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

Global contribution of pelagic fungi to protein degradation in the ocean -Breyer et al. – Microbiome

August 31, 2022

Posted on by

Human skin microbiome

[REVIEW]Staphylococcus epidermidis and its dual lifestyle in skin health and infection – Severn & Horswill – Nature Reviews Microbiology

Human oral microbiome

Effect of chewing gum containing Xylitol and blackberry powder on oral bacteria: A randomized controlled crossover trial – Miller et al. – Archives of Oral Biology

Human gut microbiome

Antimicrobial peptide production in response to gut microbiota imbalance – Cardoso et al. – Peptides

ROLE OF GUT MICROBIOTA IN DEPRESSION: UNDERSTANDING MOLECULAR PATHWAYS, RECENT RESEARCH, AND FUTURE DIRECTION – Rathour et al. – Behavioural Brain Research

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

Gut-derived metabolites influence neurodevelopmental gene expression and Wnt signaling events in a germ-free zebrafish model – Rea et al. – Microbiome

Animal microbiome (for animals in the wild)

Age as a primary driver of the gut microbial composition and function in wild harbor seals – Pacheco-Sandoval et al. – Scientific Reports

Plant, root, and soil microbiome

Biogeographical survey of soil microbiomes across sub-Saharan Africa: structure, drivers, and predicted climate-driven changes – Cowan et al. – Microbiome

Soil fungal communities show more specificity than bacteria for plant species composition in a temperate forest in China – Chen et al. – BMC Microbiology

Microbes in space

Machine learning algorithm to characterize antimicrobial resistance associated with the International Space Station surface microbiome – Madrigal et al. – Microbiome

Food microbiology

Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities – Somerville et al. – Microbiome

Bioinformatics

Crowdsourced benchmarking of taxonomic metagenome profilers: lessons learned from the sbv IMPROVER Microbiomics challenge – Poussin et al. – BMC Genomics

Microbes in the news (popular press, EurekAlert, ScienceDaily, Youtube, NPR, etc)

Newly Renamed Prokaryote Phyla Cause Uproar – Dan Robitzski – The Scientist

August 10, 2022

Posted on by

General microbiome

Microbiome-associated human genetic variants impact phenome-wide disease risk – Markowitz et al. – PNAS

Microbial risk score for capturing microbial characteristics, integrating multi-omics data, and predicting disease risk – Wang et al. – Microbiome

[REVIEW]A framework for testing the impact of co-infections on host gut microbiomes – Schmid et al. – Animal Microbiome

Human vaginal microbiome

Vaginal microbiota and personal risk factors associated with HPV status conversion—A new approach to reduce the risk of cervical cancer? – Yang et al. – PLOS One

Human gut microbiome

[REVIEW]The role of the gut microbiota in multiple sclerosis – Correale, Hohlfeld & Baranzini

Specific gut microbiota alterations in essential tremor and its difference from Parkinson’s disease – Zhang et al. – NPJ Parkinson’s Disease

Identification of clinical and ecological determinants of strain engraftment after fecal microbiota transplantation using metagenomics – Podlesny et al. – Cell Reports Medicine

Alterations in gut microbiota of esophageal squamous cell carcinoma patients – Cheung et al. – Journal of Gastroenterology and Hepatology

Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation – Federici et al. – Cell

Animal microbiome

Camel milk microbiota: A culture-independent assessment – Rahmeh et al. – Food Research International

Effect of processing on the anti-inflammatory efficacy of cocoa in a high fat diet-induced mouse model of obesity – Weikart et al. – The Journal of Nutritional Biochemistry

The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs – Gaire et al. – Microbiome

Plant, root, and soil microbiome

Soil microbial community structures are shaped by agricultural systems revealing little temporal variation – Fox, Widmer & Lüscher – Environmental Research

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

The streamwater microbiome encodes hydrologic data across scales – URycki et al. – Science of The Total Environment

Bioinformatics / Data

[PREPRINT]Lake iTag measurements over nineteen years, introducing the limony dataset – Rohwer & McMahon – bioRxiv

August 03, 2022

Posted on by

Pregnancy and early life

The abundance of Ruminococcus bromii is associated with faecal butyrate levels and atopic dermatitis in infancy – Sasaki et al. – Allergy

Human oral microbiome

Smokeless tobacco consumption induces dysbiosis of oral mycobiome: a pilot study – Sajid et al. – Applied Microbiology and Biotechnology

Human gut microbiome

The Proteome of Extracellular Vesicles Produced by the Human Gut Bacteria Bacteroides thetaiotaomicron In Vivo Is Influenced by Environmental and Host-Derived Factors – Stentz et al. – Applied and Environmental Microbiology

Improved gut microbiome recovery following drug therapy is linked to abundance and replication of probiotic strains – FitzGerald et al. – Gut Microbes

[REVIEW]Targeting microbiota-host interactions with resveratrol on cancer: Effects and potential mechanisms of action – Wang et al. – Critical Reviews in Food Science and Nutrition

Emerging frontiers of antibiotics use and their impacts on the human gut microbiome – Kumari et al. – Microbiological Research

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

Microbiota of the Pregnant Mouse: Characterization of the Bacterial Communities in the Oral Cavity, Lung, Intestine, and Vagina through Culture and DNA Sequencing – Greenberg et al. – Microbiology Spectrum

Phages and viruses

Viral biogeography of the mammalian gut and parenchymal organs – Shkoporov – Nature Microbiology

Bioinformatics

Namco: a microbiome explorer – Dietrich et al. – Microbial Genomics

MiCloud: A unified web platform for comprehensive microbiome data analysis – Gu et al. – PLOS One

August 1st, 2022

Posted on by

God morgon!

Good morning from Sweden.

Today’s digest has studies from diverse topics but the one that caught my attention is a preprint that addresses the controversial question of presence of a ‘normal blood microbiota’ in humans. The authors of this preprint analysed about 10,000 humans samples and provide evidence that there is no core blood microbiota.

A new preprint describes a unique Taleocin (a bacteriocin) from Pseudomonas syringae which defies the convention that bacteriocins have a narrow spectrum. The bacteriocin has a broad range killing activity against agriculturally important pathogens like Erwinia amylovora and Xanthomonas perforans as well as against the clinical human pathogen Salmonella choleraesuis.

Another preprint reports metabolic interactions responsible for unusually high Iron and lipid content in Geobacter sulfurreducens, a bacterium known iron reducing bacterium in the soil. Another environmental study found that human pathogens are the major carriers of antibiotic resistance genes in the Yangtze river – one of the longest in the world. This is in contrast to prevalent belief that conventional supercarriers are Enterococcus spp. and other fecal indicator bacteria.

Elsewhere in the digest is a preprint from my previous lab where my old colleagues have reported a small RNA and metal dependent mechanism that regulates the survival of Acinetobacter baumannii under oxidative stress.

As a bonus, there is a super intriguing preprint where the authors have actually provided evidence that coming up with creative and funny titles for your papers can help them gain more visibility and citations! So, all of you writing an article or planning to write one soon, this is a great tip!

I hope you will enjoy reading today’s digest and have a great week ahead!

Human gut

Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake – Zachary C. Holmes, et al., Microbiome

Near-sterile sites

Preprint: No evidence for a common blood microbiome based on a population study of 9,770 healthy humans – Cedric C.S. Tan, et al.

Water microbiome

Supercarriers of antibiotic resistome in a world’s large river – Jiawen Wang, et al., Microbiome

Oceanospirillales containing the DMSP lyase DddD are key utilisers of carbon from DMSP in coastal seawater – Jingli Liu, et al., Microbiome

Community structure of coral microbiomes is dependent on host morphology – Kathleen M. Morrow, et al., Microbiome

Preprint: The impact of primary colonizers on the community composition of river biofilm – Roshan Angoshtari, et al.

Soil microbiome

Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity – Xingyu Ma, et al., Microbiome

Animal microbiome

Host-microbiota interaction-mediated resistance to inflammatory bowel disease in pigs – Xuan Zhao, et al., Microbiome

Preprint: The differing roles of flavins and quinones in extracellular electron transfer in Lactiplantibacillus plantarum – Joe Gregory Tolar, et al.

Bacteria Hysteria

Preprint: Interspecies Killing Activity of Pseudomonas syringae Tailocins – Savannah L Weaver, et al.

Preprint: Enhanced production of natural shiga toxin by overexpressing A subunit of Stx2e in Stx2e-producing Escherichia coli isolated in South Korea – Jin Hur, et al.

Preprint: Geobacter sulfurreducens′ unique metabolism results in cells with a high iron and lipid content – Ethan T Howley, et al.

Preprint: Cloning, heterologous expression and characterization of o-phthalyl-CoA decarboxylase from phthalate degrading denitrifying bacterium – Madan Junghare

Preprint: Acinetobacter baumannii defends against oxidative stress through a Mn2+-dependent small RNA-mediated suppression of type VI secretion system – Somok Bhowmik, et al.

Techniques

Preprint: Programmable acetylation modification of bacterial proteins by a Cas12a-guided acetyltransferase – Liu yanqiang, et al.

Fun

Preprint: If this title is funny, will you cite me? Citation impacts of humour and other features of article titles in ecology and evolution – Stephen B Heard, et al.

July 26, 2022

Posted on by

Highlights!

Microbial determinants of effective donors in faecal microbiota transplantation for UC – Craig Haifer – Gut → Metagenomic and metabolomic data analysis showed that donor microbiota stability and increased species evenness were identified novel markers associated with donor sample therapeutic efficacy in Ulcerative Colitis.

A gut microbial peptide and molecular mimicry in the pathogenesis of type 1 diabetes – Khyati Girdhar – PNAS → A peptide sequence from Parabacteroides distasonis mimics an important insulin epitope, making it susceptible to generating type I diabetes in a mouse model. 

Human and General Microbiome

Gut microbiome changes in anti-N-methyl-D-aspartate receptor encephalitis patients – Jingya Wei – BMC Neurology

Effect of a bacteriocin-producing Streptococcus salivarius on the pathogen Fusobacterium nucleatum in a model of the human distal colon – Garreth W Lawrence – Gut Microbes

Identification of Gut Microbiome Metabolites via Network Pharmacology Analysis in Treating Alcoholic Liver Disease – Ki-Kwang Oh – Current Issues in Molecular Biology

Review: The Gut Microbiota: A Double Edge Sword in Endometriosis – Chandni Talwar – Biology of Reproduction

Non-Model Animal Microbiome

Hair Microbiome Diversity within and across Primate Species – Catherine Kitrinos – mSystems

Seasonal variations in the composition and diversity of gut microbiota in white-lipped deer (Cervus albirostris) – Zhangqiang You – PeerJ

Plant Microbiome

Effects of Domestication on Plant-Microbiome Interactions – Andres Gutierrez – Plant & Cell Physiology

Evaluation of protein extraction methods for metaproteomic analyses of root-associated microbes – Fernanda Salvato – Molecular Plant-Microbe Interactions

Environmental Microbiome

Absence of stress-promoted facilitation coupled with a competition decrease in the microbiome of ephemeral saline lakes – Mateu Menéndez-Serra – Ecology

Insights into the Antimicrobial Activities and Metabolomes of Aquimarina (Flavobacteriaceae, Bacteroidetes) Species from the Rare Marine Biosphere – Sandra Godinho Silva – Marine Drugs

More microbes

Correspondence: International travel, the gut microbiome, and ESBL-E coli carriage – Ye Peng – The Lancet. Microbe

An Engineered λ Phage Enables Enhanced and Strain-Specific Killing of Enterohemorrhagic Escherichia coli – Menglu Jin – Microbiology Spectrum

Bioinformatics and Microbiome Analysis Techniques

MOCHI, a comprehensive cross-platform tool for amplicon-based microbiota analysis – Jun-Jie Zheng – Bioinformatics

July 23, 2022

Posted on by

Greetings from Chile! Today, in this Digest, a variety of papers covering different subjects, such as the relationships between microbiome and C. difficile infection, new skin microbiome sampling techniques, FMT donor-recipient microbiome interplay, microbiome and biodiversity conservation, microbiome and vitamin metabolism, etc.; also, take a look at the papers from the “Bioinformatics and Microbiome Analysis Techniques” section.  

Human and General Microbiome

A 3D-printed transepidermal microprojection array for human skin microbiome sampling – Kun Liang – PNAS

Analysis of Intestinal Mycobiota of Patients with Clostridioides difficile Infection among a Prospective Inpatient Cohort – Yangchun Cao – Microbiology Spectrum

Role of gastrointestinal microbial populations, a terra incognita of the human body in the management of intestinal bowel disease and metabolic disorders – J E Vazquez Bucheli – Beneficial Microbes

The Gut Bacterial Community Potentiates Clostridioides difficile Infection Severity – Nicholas A Lesniak – mBio

The interplay of gut microbiota between donors and recipients determines the efficacy of fecal microbiota transplantation – Ruiqiao He – Gut Microbes

Gut commensals expand vitamin A metabolic capacity of the mammalian host – Maryam Bonakdar – Cell Host & Microbe

A reappraisal of microbiome dysbiosis during experimental periodontitis – Marion Arce – Molecular Oral Microbiology

Activity-based protein profiling identifies alternating activation of enzymes involved in the bifidobacterium shunt pathway or mucin degradation in the gut microbiome response to soluble dietary fiber – Bryan J Killinger – NPJ Biofilms and Microbiomes

Cooperative action of gut-microbiota-accessible carbohydrates improves host metabolic function – Sawako Tomioka – Cell Reports

Model Animal Microbiome

Key features of the genetic architecture and evolution of host-microbe interactions revealed by high-resolution genetic mapping of the mucosa-associated gut microbiome in hybrid mice – Shauni Doms – eLife

Non-Model Animal Microbiome

Metagenomic insights into the microbe-mediated B and K(2) vitamin biosynthesis in the gastrointestinal microbiome of ruminants – Qian Jiang – Microbiome

Exploring the Transient Microbe Population on Citrus Butterfly Wings – P D Kamala Jayanthi – Microbiology Spectrum

Review: Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter – Júnia Schultz – mSystems

Plant Microbiome

Plant genetic effects on microbial hubs impact host fitness in repeated field trials – Benjamin Brachi – PNAS

Review: Beneficial and pathogenic plant-microbe interactions during flooding stress – Clara Martínez-Arias – Plant, Cell & Environment

Environmental Microbiome

Review: Harnessing the microbiome to prevent global biodiversity loss – Raquel S Peixoto – Nature Microbiology

More Microbes

Proteome Exploration of Legionella pneumophila To Identify Novel Therapeutics: a Hierarchical Subtractive Genomics and Reverse Vaccinology Approach – Md Tahsin Khan – Microbiology Spectrum

Bioinformatics and Microbiome Analysis Techniques

LOCOM: A logistic regression model for testing differential abundance in compositional microbiome data with false discovery rate control – Yingtian Hu – PNAS

A metagenomic DNA sequencing assay that is robust against environmental DNA contamination – Omary Mzava – Nature Communications

Bioinformatic Analysis to Investigate Metaproteome Composition Using Trans-Proteomic Pipeline – Steven He – Current Protocols

July 18th, 2020

Posted on by
God morgon! Good morning from Sweden. Today’s digest features only three articles but I am sure everyone will enjoy reading it, especially a super interesting article highlighting the importance of older siblings on development of an individual’s airway and gut microbiota. The study asserts that having a closely aged older sibling has more impact on one’s microbiota as compared to having more than one older sibling. Another featured article demonstrates how gut microbiota can improve the quality of chicken by preventing intestinal inflammation. From animal farming we go over to plant farming. Another article in today’s digest shows how monocropping (growing the same crop over and over) negatively impacts the diversity of soil bacteria which eventually shows up as poor yield. This makes it imperative to consider the soil microbiota while taking decisions on crop cycle. I hope you will enjoy reading today’s digest and have a great week!

Human microbiome

The developing airway and gut microbiota in early life is influenced by age of older siblings – Emil Dalgaard Christensen, et al., Microbiome

Animal microbiome

Chicken jejunal microbiota improves growth performance by mitigating intestinal inflammation – Xiaolong Zhang, et al., Microbiome

Plant root and soil microbiome

Reduced chemodiversity suppresses rhizosphere microbiome functioning in the mono-cropped agroecosystems – Pengfa Li, et al., Microbiome

July 16, 2022

Posted on by

Human and General Microbiome

Advances and challenges in cataloging the human gut virome – Junhua Li – Cell Host & Microbe

Genomic diversity of genus Limosilactobacillus – Magdalena Ksiezarek – Microbial Genomics

Comparison of the respiratory tract microbiome in hospitalized COVID-19 patients with different disease severity – Jiali Chen – Journal of Medical Virology

An international report on bacterial communities in esophageal squamous cell carcinoma – Jason Nomburg – International Journal of Cancer

Beneficial Microbes and Compounds

Phenolic-rich beverages reduce bacterial TMA formation in an ex vivo-in vitro colonic fermentation model – Lisard Iglesias-Carres – Food & Function

Lactobacillus paragasseri OLL2809 Improves Depression-Like Behavior and Increases Beneficial Gut Microbes in Mice – Narumi Hashikawa-Hobara – Frontiers in Neuroscience

In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus – Linda B Oyama – NPJ Biofilms and Microbiomes

Review: How Dietary Fibre, Acting via the Gut Microbiome, Lowers Blood Pressure – Chudan Xu – Current Hypertension Reports

Review: Low FODMAP diet in irritable bowel syndrome: a review of recent clinical trials and meta-analyses – Kevin Whelan – Current Opinion in Clinical Nutrition and Metabolic Care

Review: Prebiotic effects of plant-derived (poly)phenols on host metabolism: Is there a role for short-chain fatty acids? – Perla Lopes de Freitas – Critical Reviews in Food Science and Nutrition

Animal Microbiome

Unveiling biogeographic patterns in the worldwide distributed Ceratitis capitata (medfly) using populations genomics and microbiome composition – María Belén Arias – Molecular Ecology

Differential oral microbiome in nonhuman primates from periodontitis susceptible and resistant matrilines – Jeffrey L Ebersole – Molecular Oral Microbiology

Chicken jejunal microbiota improves growth performance by mitigating intestinal inflammation – Xiaolong Zhang – Microbiome

Bioinformatics and Microbiome Analysis

Comparison Analysis of Different DNA Extraction Methods on Suitability for Long-Read Metagenomic Nanopore Sequencing – Lei Zhang – Frontiers in Cellular and Infection Microbiology

KOMB: K-core based de novo characterization of copy number variation in microbiomes – Advait Balaji – Computational and Structural Biotechnology Journal

CASPER: An Integrated Software Platform for Rapid Development of CRISPR Tools – Brian Mendoza – The CRISPR Journal

Integrating Choline and Specific Intestinal Microbiota to Classify Type 2 Diabetes in Adults: A Machine Learning Based Metagenomics Study – Qiang Zeng – Frontiers in Endocrinology

July 13, 2022

Posted on by

Today’s digest features studies on the leaf-microbiome of 🍅 and 🍓 plants (+ bumblebees and mites), human gut and wastewater resistome, and more. Happy reading!

Reproductive tract

Female reproductive tract microbiota and recurrent pregnancy loss: a nested case-control study – Pirkko Peuranpää – Reproductive BioMedicine Online

Gut microbiome

Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties – Sudarshan A. Shetty – Journal of the International Society for Microbial Ecology

*Within-patient evolution of plasmid-mediated antimicrobial resistance – Javier DelaFuente – bioRxiv

An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species – Sigal Leviatan – Nature Communications

Animal microbiome

Carpenter Bees (Xylocopa) Harbor a Distinctive Gut Microbiome Related to That of Honey Bees and Bumble Bees – Jo-anne C. Holley – Applied and Environmental Microbiology

Animal experiments

Gardnerella Exposures Alter Bladder Gene Expression and Augment Uropathogenic Escherichia coli Urinary Tract Infection in Mice – Nicole M. Gilbert – Frontiers in Cellular and Infection Microbiology

Plant microbiome

*The Greenhouse Phyllosphere Microbiome and Associations with Introduced Bumblebees and Predatory Mites – Marie Legein – Microbiology Spectrum

Food microbiome

Longitudinal, multi-platform metagenomics yields a high-quality genomic catalog and guides an in vitro model for cheese communities – Christina C. Saak – bioRxiv

New insights of bacterial communities in fermented vegetables from shotgun metagenomics and identification of antibiotic resistance genes and probiotic bacteria – Muhammad Yasir – Food Research International

Water microbiome

*High-resolution characterisation of short-term temporal variability in the taxonomic and resistome composition of wastewater influent – Kevin Kaibond Chau – bioRxiv

Pilot investigation on biostability of drinking water distribution systems under water source switching – Kejia Zhang – Applied Microbiology and Biotechnology

Bioinformatics

*BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes – Michael J. Pavia – bioRxiv

getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories – Vincent Moco – BMC Bioinformatics

baseLess: Lightweight detection of sequences in raw MinION data – Ben Noordijk – bioRxiv