Category Archives: Microbial Ecology

September 18, 2022

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Human and General Microbiome

Neisseria species as pathobionts in bronchiectasis – Liang Li – Cell Host & Microbe

The gut microbiome molecular complex in human health and disease – Paul Wilmes – Cell Host & Microbe

Codiversification of gut microbiota with humans – Taichi A Suzuki – Science

Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course – The iMSMS Consortium – Cell

Composition and diverse differences of intestinal microbiota in ulcerative colitis patients – Siying Zhu – Frontiers in Cellular and Infection Microbiology

A systematic review on omics data (metagenomics, metatranscriptomics, and metabolomics) in the role of microbiome in gallbladder disease – Paola Di Carlo – Frontiers in Physiology

Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases – Gianluca Ianiro – Nature Medicine

Drivers and determinants of strain dynamics following fecal microbiota transplantation – Thomas S B Schmidt – Nature Medicine

Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects – Jonathan T L Kang – Nature Microbiology

Structural and functional dysbiosis of gut microbiota in Tibetan subjects with coronary heart disease – Qi Cheng – Genomics

Growth of succinate consumer Dialister hominis is supported by Bacteroides thetaiotaomicron – Mitsuo Sakamoto – Anaerobe

RhoB affects colitis through modulating cell signaling and intestinal microbiome – Jianming Yang – Microbiome

Review: Diet fuelling inflammatory bowel diseases: preclinical and clinical concepts – Timon E Adolph – Gut

Review: Recent findings in Akkermansia muciniphila-regulated metabolism and its role in intestinal diseases – Meng-Jie Liu – Clinical Nutrition

Beneficial Microbes and Compounds

Comprehensive analysis of microbiome, metabolome and transcriptome revealed the mechanisms of Moringa oleifera polysaccharide on preventing ulcerative colitis – Hanchen Tian – International Journal of Biological Macromolecules

Probiotics ameliorates pulmonary inflammation via modulating gut microbiota and rectifying Th17/Treg imbalance in a rat model of PM2.5 induced lung injury – Yongcan Wu – Ecotoxicology and Environmental Safety

Short-term supplementation with ω-3 polyunsaturated fatty acids modulates primarily mucolytic species from the gut luminal mucin niche in a human fermentation system – Charlène Roussel – Gut Microbes

Model Animal Microbiome

Interactive Effect of Combined Intermittent and Sustained Hypoxia and High-Fat Diet on the Colonic Mucosal Microbiome and Host Gene Expression in Mice – Saif Mashaqi – Nature and Science of Sleep

Non-Model Animal Microbiome

Fungi are more transient than bacteria in caterpillar gut microbiomes – Martin Šigut – Scientific Reports

Adapting to climate with limited genetic diversity: Nucleotide, DNA methylation and microbiome variation among populations of the social spider Stegodyphus dumicola – Anne Aagaard – Molecular Ecology

Bioinformatics and Microbiome Analysis

Filtering ASVs/OTUs via mutual information-based microbiome network analysis – Elham Bayat Mokhtari – BMC Bioinformatics

Batch effects removal for microbiome data via conditional quantile regression – Wodan Ling – Nature Communications

Phylogenetic Analysis of Anti-CRISPR and Member Addition in the Families – Sweta Nidhi – Molecular Biotechnology

Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights – Mason R Stothart – Molecular Ecology Resources

SnapShot: The Expobiome Map – Velma T E Aho – Cell Host & Microbe

September 9, 2022

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The #MVIF Season 2 is starting NEXT WEEK!

With the new starting time to better accommodate extra time zones &
highlights will be hosted by @gather_town for more engaging personal interaction & networking (from October).

Resistome

Capturing the antibiotic resistome of preterm infants reveals new benefits of probiotic supplementation – Allison K. Guitor – Microbiome

Review: Soil microbiomes and one health – Samiran Banerjee & Marcel G. A. van der Heijden – Nature Reviews Microbiology

Oral microbiome

Corncob structures in dental plaque reveal microhabitat taxon specificity – Viviana Morillo-Lopez – Microbiome

Vaginal microbiome

Heritable vaginal bacteria influence immune tolerance and relate to early-life markers of allergic sensitization in infancy – Kathryn E.McCauley – Cell Reports Medicine

Gut virome/microbiome

Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort – Suguru Nishijima – Nature Communications

Review: Mutualistic interplay between bacteriophages and bacteria in the human gut – Andrey N. Shkoporov – Nature Reviews Microbiology

Identification of trypsin-degrading commensals in the large intestine – Youxian Li – Nature

Microbiota imbalance induced by dietary sugar disrupts immune-mediated protection from metabolic syndrome – Yoshinaga Kawano – Cell

Design, construction, and in vivo augmentation of a complex gut microbiome – Alice G. Cheng – Cell

Plant, root and soil microbiome

Source and acquisition of rhizosphere microbes in Antarctic vascular plants – Sergio Guajardo-Leiva – Frontiers in Microbiology

Animal microbiome

Individual variation in the avian gut microbiota: the influence of host state and environmental heterogeneity – Shane E. Somers – bioRxiv

Animal experiment

From germ-free to wild: modulating microbiome complexity to understand mucosal immunology – Carolyn A. Thomson – Mucosal Immunology

September 8, 2022

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Today’s microbiome digest includes ten rules for teaching yourself R, food safety profiles of ready-to-eat raw minced meat, teaching that addresses eco-anxiety, as well as both pathogenic and entomopathogenic fungi!

Human gut microbiome

Meals, Microbiota and Mental Health in Children and Adolescents (MMM-Study): A protocol for an observational longitudinal case-control study – Asbjornsdottir et al. – PLOS One

Strongyloides stercoralis infection induces gut dysbiosis in chronic kidney disease patients – Hai et al. – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Mycoparasitism capability and growth inhibition activity of Clonostachys rosea isolates against fungal pathogens of grapevine trunk diseases suggest potential for biocontrol – Geiger et al. – PLOS One

Impact of endophytic colonization by entomopathogenic fungi on the behavior and life history of the tobacco peach aphid Myzus persicae var. nicotianae – Wilberts et al. – PLOS One

Food microbiology

Bacteriological quality and antimicrobial susceptibility profiles of isolates of ready-to-eat raw minced meat from hotels and restaurants in Arba Minch, Ethiopia – Tonjo et al. – PLOS One

Bioinformatics

Ten simple rules for teaching yourself R – Lawlor et al. – PLOS Computational Biology

Techniques

Laboratory evaluation of RealStar Yellow Fever Virus RT-PCR kit 1.0 for potential use in the global yellow fever laboratory network – Basile et al. – PLOS Neglected Tropical Diseases

Science, publishing, and career )

Insufficient yet improving involvement of the global south in top sustainability science publications – Dangles et al. – PLOS One

Adapt conservation biology teaching to address eco-anxiety in students – São Pedro et al. – PLOS Biology

August 24, 2022

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General microbiome

[REVIEW]Detecting bacterial adaptation within individual microbiomes – Liebermann – Phil. Trans. R. Soc. B

[REVIEW]Soil microbiomes and one health – Banerjee & van der Heijden – Nature Reviews Microbiology

Pregnancy and early life

Microbial Analysis of Umbilical Cord Blood Reveals Novel Pathogens Associated with Stillbirth and Early Preterm Birth – Vander Haar et al. – mBio

Human respiratory microbiome

The respiratory microbiota alpha-diversity in chronic lung diseases: first systematic review and meta-analysis – Avalos-Fernandez et al. – Respiratory Research

Human saliva microbiome

Saliva microbiome, dietary, and genetic markers are associated with suicidal ideation in university students – Ahrens et al. – Scientific Reports

Human gut microbiome

The gut microbiota is associated with immune cell dynamics in humans – Schluter et al. – Nature

The systemic anti-microbiota IgG repertoire can identify gut bacteria that translocate across gut barrier surfaces – Vujkovic-Cvijin et al. – Science Translational Medicine

Higher pathogen load in children from Mozambique vs. USA revealed by comparative fecal microbiome profiling – Kim et al. – ISME Communications

Correlation of inflammatory biomarkers with the diversity of Bacteroidaceae, Bifidobacteriaceae, Prevotellaceae and Lactobacillaceae families in the intestinal microbiota of patients with end stage renal disease – Asgharian et al. – Advances in Medical Sciences

Impact of the Host Microbiome on Vaccine Responsiveness: Lessons Learned and Future Perspective – Stefanetti & Kasper – Biochemistry

Location-specific signatures of Crohn’s disease at a multi-omics scale – Gonzalez et al. – Microbiome

Association of food insecurity on gut microbiome and metabolome profiles in a diverse college-based sample – Mohr et al. – Scientific Reports

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

The Diversity and Functional Capacity of Microbes Associated with Coastal Macrophytes – Miranda et al. – mSystems

Microbes in space

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

Bioinformatics

[PREPRINT]Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4 – Blanco-Miguez et al. – bioRxiv

Linear and nonlinear correlation estimators unveil undescribed taxa interactions in microbiome data – Lin, Eggesbø & Peddada – Nature Communications

Techniques

Primers matter: Influence of the primer selection on human fungal detection using high throughput sequencing – Wiemann et al. – Gut Microbes

Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples – Baker et al. – mSystems

August 19, 2022

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Today’s digest is short and sweet! We have articles on the gut microbiota in rats, the influence of host genetics on the leaf fungal microbiome, and biofilm fouling in drinking water. There are also two manuscripts which provide tips for pathway enrichment analysis and biomarker discovery.

Happy reading! Also, if you’re in Scotland, consider checking out the enormous E. coli in Edinburgh this weekend!

Animal experiments

Effects of sea salt intake on metabolites, steroid hormones, and gut microbiota in rats – Chanmuang et al. – PLOS One

Plant, root, and soil microbiome

The changing influence of host genetics on the leaf fungal microbiome throughout plant development – Karasov & Lundberg – PLOS Biology

Water and extremophile microbiome

Impacts of temperature and hydraulic regime on discolouration and biofilm fouling in drinking water distribution systems – Fish et al. – PLOS Water

Bioinformatics

Nine quick tips for pathway enrichment analysis – Chicco & Agapito – PLOS Computational Biology

Ten quick tips for biomarker discovery and validation analyses using machine learning – Diaz-Uriarte et al. – PLOS Computational Biology

August 5, 2022

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Today’s digest is brief and includes research examining the association between the gut microbiota and Gulf War illness, determining the distribution of psychrophilic microorganisms in a beef slaughterhouse, measuring the quality of DNA sequences via degradation, and more.

Happy Friday!

General microbiome

Measuring quality of DNA sequence data via degradation – Karr et al. – PLOS One

Atypical integrative element with strand-biased circularization activity assists interspecies antimicrobial resistance gene transfer from Vibrio alfacsensis – Nonaka et al. – PLOS One

Human vaginal microbiome

Association of key species of vaginal bacteria of recurrent bacterial vaginosis patients before and after oral metronidazole therapy with short- and long-term clinical outcomes – Mollin et al. – PLOS One

Human gut microbiome

Examining the association between the gastrointestinal microbiota and Gulf War illness: A prospective cohort study – Kates et al. – PLOS One

Food microbiology

Distribution of psychrophilic microorganisms in a beef slaughterhouse in Japan after cleaning – Nakamura et al. – PLOS One

Science, publishing, and career

Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses – Bacon et al. – PLOS Computational Biology

July 28, 2022

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Today’s digest includes research on the gut microbiome of infants, ruminants, and sand flies! There is also a preprint about sewage microbiomes as well as a research article about photosynthetic bacterial communities in crop fields.

Happy reading!

Human skin microbiome

Lichen Planopilaris: The first biopsy layer microbiota inspection – Pinto et al. – PLOS One

Human gut microbiome

Adaptation of the infant gut microbiome during the complementary feeding transition – McKeen et al. – PLOS One

Animal microbiome

Metagenomic insights into the microbe-mediated B and K2 vitamin biosynthesis in the gastrointestinal microbiome of ruminants – Jiang et al. – Microbiome

Comparative analysis of the gut microbiota of sand fly vectors of zoonotic visceral leishmaniasis (ZVL) in Iran; host-environment interplay shapes diversity – Karimian et al. – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Metagenomic analysis of the dynamical conversion of photosynthetic bacterial communities in different crop fields over different growth periods – Cheng et al. – PLOS One

Built environment

Preprint: A metagenomic investigation of spatial and temporal changes in sewage microbiomes across a university campus – Fierer et al. – bioRxiv

July 14, 2022

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Today’s digest has multiple articles on statistical and bioinformatic techniques! Also included is a job ad from my research team, so check it out if you’re interested in gaining geomicrobiology research experience at a national laboratory.

Events and jobs

Our geomicrobiology research group at the National Energy Technology Lab – Pittsburgh is looking for a technician/researcher. Exact responsibilities are somewhat flexible depending on interest and education-level; we are accepting applications from current students at all levels as well as postdocs.

General microbiome

Mycobacteriophages: From Petri dish to patient – Hatfull – PLOS Pathogens

Animal microbiome

Reconstructing the ecosystem context of a species: Honey-borne DNA reveals the roles of the honeybee – Wirta et al. – PLOS One

Plant, root, and soil microbiome

Patterns of microbial communities were shaped by bioavailable P along the elevation gradient of Shergyla Mountain, as determined by analysis of phospholipid fatty acids – Ba et al. – PLOS One

Preprint: Soil chemistry and soil history significantly structure oomycete communities in Brassicaceae crop rotations – Blakney et al. – bioRxiv

Community succession and straw degradation characteristics using a microbial decomposer at low temperature – Zhang et al. – PLOS One

Built Environment

Indoor air microbial load, antibiotic susceptibility profiles of bacteria, and associated factors in different wards of Arba Minch General Hospital, southern Ethiopia – Kayta et al. – PLOS One

Techniques

moreThanANOVA: A user-friendly Shiny/R application for exploring and comparing data with interactive visualization – Jiang et al. – PLOS One

Preparation of biological monolayers for producing high-resolution scanning electron micrographs – Mentor et al. – PLOS One

The accuracy of absolute differential abundance analysis from relative count data – Roche & Mukherjee – PLOS Computational Biology

AC-PCoA: Adjustment for confounding factors using principal coordinate analysis – Wang et al. – PLOS Computational Biology

Microbes in the news

The Art of Science: Students Participate in University’s First-Ever Bio-Art Class – Bernardi – Syracuse University News

July 13, 2022

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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

July 12, 2022

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Human and General Microbiome

Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections – Paula Hayakawa Serpa – Genome Medicine

Alterations in gut microbiota of esophageal squamous cell carcinoma patients – Man Kit Cheung – Journal of Gastroenterology and Hepatology

Altered Pattern of Immunoglobulin A-Targeted Microbiota in Inflammatory Bowel Disease After Fecal Transplantation – Wen-Qi Huang – Frontiers in Microbiology

16S rRNA gene sequencing reveals an altered composition of gut microbiota in children with Mycoplasma pneumoniae pneumonia treated with azithromycin – Qiong Deng – The Journal of General and Applied Microbiology

Clinical and metagenomic profiling of hormonal acne-prone skin in different populations – Nina Hrapovic – Journal of Cosmetic Dermatology

Microbiota diversity in nonalcoholic fatty liver disease and in drug-induced liver injury – Cristina Rodriguez-Diaza – Pharmacological Research

Beneficial Microbes and Compounds

Review: The potential role of prebiotics, probiotics, and synbiotics in adjuvant cancer therapy especially colorectal cancer – Zahoor Alam – Journal of Food Biochemistry

Review: Probiotics, prebiotics and postbiotics for better sleep quality: a narrative review – J E Haarhuis – Beneficial Microbes

Review: Gut Microbiota: A Novel Therapeutic Target for Parkinson’s Disease – Manlian Zhu – Frontiers in Immunology

Animal Model Microbiome

Obesity enriches for tumor protective microbial metabolites and treatment refractory cells to confer therapy resistance in PDAC – Kousik Kesh – Gut Microbes

Profiling of d-alanine production by the microbial isolates of rat gut microbiota – Cindy J. Lee – The FASEB Journal

Non-Model Animal Microbiome

Within-community variation of interspecific divergence patterns in passerine gut microbiota – Jan Kubovčiak – Ecology and Evolution

Bacteriophages

Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria – Brian Y. Hsueh – Nature Microbiology

Bioinformatics and Microbiome Analysis

Preprint: CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning – Alex Chklovski – biorXiv

Cancer type classification using plasma cell-free RNAs derived from human and microbes – Shanwen Chen – eLife

Temporal Alignment of Longitudinal Microbiome Data – Ran Armoni – Frontiers in Microbiology

A Bottom-up Approach to Testing Hypotheses That Have a Branching Tree Dependence Structure, with Error Rate Control – Yunxiao Li – Journal of the American Statistical Association