Category Archives: Resistome

May 12, 2023

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Today’s digest features studies on human respiratory tract, mouse models, bovine milk microbiome, and more. See you at #MVIF next week!

Respiratory tract microbiome

Review: Ecology of the respiratory tract microbiome – Ana Elena Pérez-Cobas – Trends in Microbiology

Cervicovaginal microbiome

The cervical microbiota of Hispanics living in Puerto Rico is highly volatile and dominated by Lactobacillus iners regardless of HPV status – Daniela Vargas-Robles – bioRxiv

Gut microbiome

Key determinants of success in fecal microbiota transplantation: From microbiome to clinic – Serena Porcari – Cell Host & Microbes

Profiling the human intestinal environment under physiological conditions – Dari Shalon – Nature

Interaction between gut microbiota and sex hormones and their relation to sexual dimorphism in metabolic diseases – Jose Antonio Santos-Marcos – Biology of Sex Differences

Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis – Paige Salerno – bioRxiv

Animal microbiome

Metagenomic analysis of milk microbiota in the bovine subclinical mastitis – Giulia Alessandri – bioRxiv

Animal experiments

MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice – Paolo Manghi – Cell Reports

Bioinformatics

ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning – Olga Mineeva – Plos Computational Biology

Technique

Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing – David Calderón-Franco – Antonie van Leeuwenhoek

Built environment

The microbiome of an outpatient rehabilitation clinic and predictors of contamination: A pilot study – Gabriella Brigando – PlosOne

April 14, 2023

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Today’s reading recommendation includes microbiome from sites with low anthropogenic impact, drinking water microbiome, and more.

If you have only a minute for reading then your must read is this amazing summary thread on how you should be careful with making assumptions ⬇️

See you at #MVIF next week!

Global resistome

Global trends in antimicrobial resistance on organic and conventional farms – Eldon Ager – bioRxiv

*Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance? – Uli Klümper – bioRxiv

Mother-to-infant microbiome

Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites – Debby Bogaert – Cell Host & Microbe

Human gut microbiome

The Local Tumor Microbiome Is Associated with Survival in Late-Stage Colorectal Cancer Patients – Justine W. Debelius – Microbiology Spectrum

Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy – Ruben Ladeira, Julien Tap, Muriel Derrien – Microbiome Research Reports

Water microbiome

The microbial dark matter and “wanted list” in worldwide wastewater treatment plants – Yulin Zhang – Microbiome

*Microbiome, resistome and mobilome of chlorine-free drinking water treatment systems – David Calderón-Franco – Water Research

Animal experiment

Probiotics of Lacticaseibacillus paracasei SD1 and Lacticaseibacillus rhamnosus SD11 attenuate inflammation and β-cell death in streptozotocin-induced type 1 diabetic mice – Jongdee Nopparat – PlosOne

Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem – Madeleine Spatz – Microbiome

*Experimental Factors Influence Diversity Metrics of the Gut Microbiome in Laboratory Mice – Rikeish R. Muralitharan – bioRxiv

Virome & phages

Expanding known viral diversity in the healthy infant gut – Shiraz A. Shah – Nature Microbiology

Large-scale phage cultivation for commensal human gut bacteria – Juntao Shen – Cell Host & Microbe

Methodology

Reducing bias in microbiome research: Comparing methods from sample collection to sequencing – Jolanda Kool – Frontiers in Microbiology

In Vitro Modelling of Oral Microbial Invasion in the Human Colon – Lucie Etienne-Mesmin – Microbiology Spectrum

Bioinformatics

Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes – Wojtek Bazant – Microbiome

March 9, 2023

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Today’s digest features studies on latent and established antibiotic resistance genes in microbiomes, newborn skin microbiome, drinking water microbiome after COVID-19 pandemic, and more. Listen to the science behind The Last of Us!

See you at #MVIF next week!

Antibiotic resistome

*Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes – Juan Salvador Inda-Díaz – Microbiome

Human skin

*The skin microbiome in the first year of life and its association with atopic dermatitis – Alexis Rapin – Allergy

Urinary tract

Review: Microbiome in urological diseases: Axis crosstalk and bladder disorders – Hae Woong Choi – Investigative and Clinical Urology

Human gut

Human microbiome variance is underestimated – Fergus Shanahan – Current Opinion in Microbiology

Population-level impacts of antibiotic usage on the human gut microbiome – Kihyun Lee – Nature Communications

Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut – Nick Bohmann – bioRxiv

Review: Milk glycan metabolism by intestinal bifidobacteria: insights from comparative genomics – Aleksandr A. Arzamasov & Andrei L. Osterman – Critical Reviews in Biochemistry and Molecular Biology

Guts Imbalance Imbalances the Brain: A Review of Gut Microbiota Association With Neurological and Psychiatric Disorders – Laura Mitrea – Frontiers in Medicine

Drinking water

*Gradual Recovery of Building Plumbing-Associated Microbial Communities after Extended Periods of Altered Water Demand during the COVID-19 Pandemic – Solize Vosloo – Environmental Science & Technology

February 13, 2023

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Today’s reading recommendation is a microbiota review collection edited by Lindsay Hall and Melanie Schirmer.

Happy Monday and see you at #MVIF!

Vaginal microbiome

Gardnerella Diversity and Ecology in Pregnancy and Preterm Birth – Hanna L. Berman – bioRxiv

Heterogeneity of the group B streptococcal type VII secretion system and influence on colonization of the female genital tract – Brady L. Spencer – bioRxiv

Urinary microbiome

Comparative Genomic Study of Streptococcus anginosus Reveals Distinct Group of Urinary Strains – Ananya Prasad – mSphere

Human gut

Gut microbes predominantly act as symbiotic partners rather than raw nutrients – Nuno Felipe da Silva Soares – bioRxiv

Antibiotic resistance in the commensal human gut microbiota – Lisa E Lamberte, Willem van Schaik – Current Opinion in Microbiology

Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting – Lharbi Dridi – Nature Communications

Animal experiments

Over supplementation with vitamin B12 alters microbe-host interactions in the gut leading to accelerated Citrobacter rodentium colonization and pathogenesis in mice – Andrew J. Forgie – Microbiome

Disturbance of lipid metabolism in germ-free mice transplanted with gut microbiota of DSS-induced colitis mice – Chungho Lee – Plos One

Bioinformatics

Accurate and fast graph-based pangenome annotation and clustering with ggCaller – Samuel T. Horsfield – bioRxiv

Brief report: uBin – a manual refining tool for genomes from metagenomes – Till L V Bornemann – Environmental Microbiology

In-situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day – Javier Tamames – bioRxiv

The virtual microbiome: A computational framework to evaluate microbiome analyses – Belén Serrano-Antón – Plos One

January 13, 2023

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The very first 2023 digest features HMOs, antimicrobials and the neonatal gut microbiota, cheese community, cow rumen microbiome, SemiBin2, and more. Happy Friday and see you next week at #MVIF!

Food microbiome

*Longitudinal, Multi-Platform Metagenomics Yields a High-Quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities – Christina C. Saak – mSystems

Gut microbiome

*Human milk oligosaccharides, antimicrobial drugs, and the gut microbiota of term neonates: observations from the KOALA birth cohort study – D.J.M Barnett – Gut microbes

The gut microbiota in multiple sclerosis varies with disease activity – Florence Thirion – Genome Medicine

Review: Intestinal gas production by the gut microbiota: A review – Erasme Mutuyemungu – Journal of Functional Foods

Gestational diabetes is driven by microbiota-induced inflammation months before diagnosis – Yishay Pinto – Gut

Review: The gut microbiota is an emerging target for improving brain health during ageing – Marcus Boehme – Gut microbiome

Vaginal microbiome

Commensal Lactobacilli Metabolically Contribute to Cervical Epithelial Homeostasis in a Species-Specific Manner – Nicole R. Jimenez – mSphere

Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome – William F. Kindschuh – Nature Microbiology

Animal experiment

Gut microbiota of the young ameliorates physical fitness of the aged in mice – Kwang H. Kim – Microbiome

Catheterization of mice triggers resurgent urinary tract infection seeded by a bladder reservoir of Acinetobacter baumannii – Jennie E. Hazen – Science Translational Medicine

Prebiotic intervention with HAMSAB in untreated essential hypertensive patients assessed in a phase II randomized trial – Hamdi A. Jama – Nature Cardiovascular Research

Akkermansia muciniphila protects mice against an emerging tick-borne viral pathogen – Jinyan Xie – Nature Microbiology

Animal microbiome

Beehives possess their own distinct microbiomes – Lorenzo A. Santorelli – Environmental Microbiome

*Differential carbon utilization enables co-existence of recently speciated Campylobacteraceae in the cow rumen epithelial microbiome – Cameron R. Strachan – Nature Microbiology

Bioinformatics

Ecological landscapes guide the assembly of optimal microbial communities – Ashish B. George and Kirill S. Korolev – Plos Computational Biology

Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering – Theresa Ullmann – Plos Computational Biology

Ten simple rules for using public biological data for your research – Vishal H. Oza – Plos Computational Biology

*SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing – Shaojun Pan – bioRxiv

December 9, 2022

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Today’s digest features global antimicrobial resistance, comammox and anammox bacteria in wastewater treatment, mOTUs3, and more. Check out Elisa Granato & Christoph Ziegenhain’s story about postdoc life. Happy Friday and see you next week at #MVIF!

Global microbiome & resistome

Experimental temperatures shape host microbiome diversity and composition – Jingdi Li – Global Change Biology

Global biogeography and projection of soil antibiotic resistance genes – Zheng et al. – Science Advances

*Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance – Patrick Munk – Nature Communications

Blood microbiome

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

Gut microbiome

Effects of dog ownership on the gut microbiota of elderly owners – Chaona Jiang – Plos One

Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases – Yoshihiko Tomofuji – Cell Genomics

Gut microbiome-wide association study of depressive symptoms – Djawad Radjabzadeh – Nature Communications

Development of non-alcoholic steatohepatitis is associated with gut microbiota but not oxysterol synthesis – Jacqueline Wyss – bioRxiv

The microbiome’s fiber degradation profile and its relationship with the host diet – Yotam Cohen & Elhanan Borenstein – BMC Biology

Animal microbiome

Lactobacillus reuteri improves the development and maturation of fecal microbiota in piglets through mother-to-infant microbe and metabolite vertical transmission – Gang Wang – Microbiome

Live biotherapeutics

Development of a live biotherapeutic throat spray with lactobacilli targeting respiratory viral infections – Irina Spacova – Microbial Biotechnology

Soil/root/plant microbiome

Differential microbial assembly processes and co-occurrence networks in the soil-root continuum along an environmental gradient – Yangquanwei Zhong – iMeta

Water microbiome

*Co-occurrence and cooperation between comammox and anammox bacteria in a full-scale attached growth municipal wastewater treatment process – Katherine J Vilardi – bioRxiv

Full-scale activated sludge transplantation reveals a highly resilient community structure – Giulia Dottorini – Water Research

Bioinformatics

Towards complete representation of bacterial contents in metagenomic samples – Xiaowen Feng, Heng Li – arXiv

*Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments – Hans-Joachim Ruscheweyh – Microbiome

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023 – CNCB-NGDC Members and Partners – Nucleic Acids Research

Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes – Lei Liu – Microbiome

November 4, 2022

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Today’s digest features a 30-color colorblind friendly color palette and functions for mapping color to hierarchical/nested data, ecosystem-specific reference databases, stoma samples for a very effective way of small intestinal microbiome characterization, and a reminder that 16S rRNA gene sequencing is NOT metagenomics. Happy Friday!

Join the next #MVIF when Sarah Lebeer will talk about citizen science and vaginal microbiome!!

Global resistome

Sharing of Antimicrobial Resistance Genes between Humans and Food Animals – Huiluo Cao – mSystems

Gut microbiome

Host-microbiome interactions: Gut-Liver axis and its connection with other organs – Swadha Anand & Sharmila S. Mande – npj Biofilms and Microbiomes

Gut microbiota bacterial strain richness is species specific and limits therapeutic engraftment – Alice Chen-Liaw – bioRxiv

Effects of different amoxicillin treatment durations on microbiome diversity and composition in the gut – Katrine Lekang – Plos One

The microbiota promotes social behavior by modulating microglial remodeling of forebrain neurons – Joseph J. Bruckner – Plos Biology

Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants – Lauren C. Beck – Nature Microbiology

*Plasticity of the adult human small intestinal stoma microbiota – Bahtiyar Yilmaz – Cell Host & Microbe


Bioinformatics

MIDAS2: Metagenomic Intra-species Diversity Analysis System – Chunyu Zhao – Bioinformatics

Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data – Matteo Ciciani – Nature Communications

*microshades: An R Package for Improving Color Accessibility and Organization of Microbiome Data – Erin M. Dahl – Microbiology Resource Announcements

*Application of ecosystem-specific reference databases for increased taxonomic resolution in soil microbial profiling – Christina Karmisholt Overgaard – Frontiers in Microbiology


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

August 1st, 2022

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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 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