Category Archives: Resistome

May 28, 2022

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Highlights!

Recently, Science released a special issue about microbiomes, with the following articles:

Human and General Microbiome  

Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes – Adair L Borges – Nature Microbiology

Characteristics of the gut microbiota in women with premenstrual symptoms: A cross-sectional study – Takashi Takeda – PloS ONE

Dynamic colonization of gut microbiota and its influencing factors among the breast-feeding infants during the first two years of life – Ping Li – Journal of Microbiology

Metabolomics analysis reveals molecular linkages for the impact of vitamin D on childhood allergic airway diseases – Yu-Ho Chang – Pediatric Allergy and Immunology

Lysophosphatidylserines derived from microbiota in Crohn’s disease elicit pathological Th1 response – Yuriko Otake-Kasamoto – Journal of Experimental Medicine 

Tumor tissue-specific bacterial biomarker panel for colorectal cancer: Bacteroides massiliensis, Alistipes species, Alistipes onderdonkii, Bifidobacterium pseudocatenulatum, Corynebacterium appendicis – Rizwana Hasan – Archives of Microbiology

Lung Microbiota of Critically Ill COVID-19 Patients are Associated with Non-Resolving Acute Respiratory Distress Syndrome – Robert F J Kullberg – American Journal of Respiratory and Critical care Medicine

Altered Gut Microbiome in Patients With Dermatomyositis – Sangmee Sharon Bae – ACR Open Rheumatology

Review: Importance of crosstalk between the microbiota and the neuroimmune system for tissue homeostasis – Kunyu Li – Clinical & Translational Immunology

Review: Dietary influences on symptomatic and non-symptomatic toxicities during cancer treatment: A narrative review – Alan J Kim – Cancer Treatment Reviews

Review: How can patients with Clostridioides difficile infection on concomitant antibiotic treatment be best managed? – Fidelma Fitzpatrick – The Lancet. Infectious Diseases

Model Animal Microbiome

Protocol: Mouse Model to Study Salmonella-Induced Colitis – Katrin Ehrhardt – Methods in Molecular Biology

Amino acid-balanced diets improved DSS-induced colitis by alleviating inflammation and regulating gut microbiota – Sen Li – European Journal of Nutrition

Excess growth hormone alters the male mouse gut microbiome in an age-dependent manner – Elizabeth A Jensen – Endocrinology

Non-Model Animal Microbiome

Metagenomic Analysis of the Gastrointestinal Microbiota of Gadus morhua callarias L. Originating from a Chemical Munition Dump Site – Wojciech Wilczynski – Toxics

Bacterial Symbionts in Ceratitis capitata – Alessia Cappelli – Insects

Egg microbiota is the starting point of hatchling gut microbiota in the endangered yellow-spotted Amazon river turtle – Ana Sofia Carranco – Molecular Ecology

Unveiling the egg microbiota of the loggerhead sea turtle Caretta caretta in nesting beaches of the Mediterranean Sea – Luca Vecchioni – PloS ONE

Comparative Analyses of Scylla olivacea Gut Microbiota Composition and Function Suggest the Capacity for Polyunsaturated Fatty Acid Biosynthesis – Nyok-Sean Lau – Microbial Ecology

Global landscape of gut microbiome diversity and antibiotic resistomes across vertebrates – Guangping Huang – The Science of the Total Environment

Beneficial Microbes and Compounds

Review: Functional fermented probiotics, prebiotics and synbiotics from non-dairy products: A perspective from nutraceutical – Dharmendra Kumar – Molecular Nutrition & Food Research

Bifidobacterium longum CCFM752 prevented hypertension and aortic lesion, improved antioxidative ability, and regulated the gut microbiome in spontaneously hypertensive rats – Wenwei Lu – Food & Function

Intestinal Flora Mediates Antiobesity Effect of Rutin in High-Fat-Diet Mice – Xu Yan – Molecular Nutrition & Food Research

Multi-Probiotics ameliorate Major depressive disorder and accompanying gastrointestinal syndromes via serotonergic system regulation – Peijun Tian – Journal of Advanced Research

Butyrate, a postbiotic of intestinal bacteria, affects pancreatic cancer and gemcitabine response in in vitro and in vivo models – Concetta Panebianco – Biomedicine & Pharmacotherapy

Plant and Fungi Microbiome

Deciphering core phyllomicrobiome assemblage on rice genotypes grown in contrasting agroclimatic zones: implications for phyllomicrobiome engineering against blast disease – Kuleshwar Prasad Sahu – Environmental Microbiome

Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts – Sunde Xu – Nature Microbiology

Other studies

Indoor microbiome, microbial and plant metabolites, chemical compounds and asthma symptoms in junior high school students: a multicentre association study in Malaysia – Yu Sun – The European Respiratory Journal

Comparative Analysis of Metagenomics and Metataxonomics for the Characterization of Vermicompost Microbiomes – Marcos Pérez-Losada – Frontiers in Microbiology

April 20, 2022

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General microbiome

How the gut talks to the brain – Adamantidis – Science

Pregnancy and early life

Relationship between gut microbiome characteristics and the effect of nutritional therapy on glycemic control in pregnant women with gestational diabetes mellitus – Chen et al. – PLOS One

Dynamics of the infant gut microbiota in the first 18 months of life: the impact of maternal HIV infection and breastfeeding – Grant-Beurmann et al. – Microbiome

Human respiratory microbiome

The diagnostic value of nasal microbiota and clinical parameters in a multi-parametric prediction model to differentiate bacterial versus viral infections in lower respiratory tract infections – Li et al. – PLOS One

Human skin microbiome

The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes – Verbanic, Deacon & Chen – Microbiology Spectrum

Human vaginal microbiome

Vaginal microbiota as an unusual cause of spondylodiscitis – Kolakowska et al. – Archives of Gynecology and Obstetrics

Human gut microbiome

Environmental factors shaping the gut microbiome in a Dutch population – Gacesa et al. – Nature

Predictive Role of Gut Microbiota in Weight Loss Achievement after Bariatric Surgery – Gutierrez-Repiso et al. – Journal of the American College of Surgeons

Intestinal Blautia may protect against neutropenic fever in allogeneic transplant patients by augmenting the intestinal epithelium – Rashidi et al. – Clinical Infectious Diseases

Clinical Observation of the Effects of Oral Opioid on Inflammatory Cytokines and Gut Microbiota in Patients with Moderate to Severe Cancer Pain: A Retrospective Cohort Study – Wang et al. – Pain and Therapy

The human gut microbiota contributes to type-2 diabetes non-resolution 5-years after Roux-en-Y gastric bypass – Debedat et al. – Gut Microbes

The gut microbial metabolite formate exacerbates colorectal cancer progression – Ternes et al. – Nature Metabolism

Drinking water chlorination has minor effects on the intestinal flora and resistomes of Bangladeshi children – Nadimpalli et al. – Nature Microbiology

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

The microbiota-gut-brain axis participates in chronic cerebral hypoperfusion by disrupting the metabolism of short-chain fatty acids – Xiao et al. – Microbiome

Effect of gluten-free diet and antibiotics on murine gut microbiota and immune response to tetanus vaccination – Kihl et al. – PLOS One

Hawk tea prevents high-fat diet-induced obesity in mice by activating the AMPK/ACC/SREBP1c signaling pathways and regulating the gut microbiota – Tao et al. – Food & Function

Changes in gut microbiota, metabolite SCFAs, and GPR43 expression in obese diabetic mice after sleeve gastrectomy – Guo et al. – Journal of Applied Microbiology

The gut microbiome influences host diet selection behavior – Trevelline & Kohl – PNAS

High-fat diet disrupts REG3γ and gut microbial rhythms promoting metabolic dysfunction – Frazier et al. – Cell Host & Microbe

Animal microbiome (for animals in the wild)

Intrinsic and extrinsic factors influence on an omnivore’s gut microbiome – Trujillo et al. – PLOS One

Effects of Schyzocotyle acheilognathi (Yamaguti, 1934) infection on the intestinal microbiota, growth and immune reactions of grass carp (Ctenopharyngodon idella) – Fu et al. – PLOS One

Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses – Shan et al. – Microbiome

Interspecies microbiome transplantation recapitulates microbial acquisition in mosquitoes – Coon, Hedge & Hughes

Gut microbiota promote biotransformation and bioaccumulation of arsenic in tilapia – Environmental Pollution

Plant, root, and soil microbiome

Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis thaliana aerial growth and responses to auxin, ethylene, and reactive oxygen species – Vandepol et al. – PLOS One

Bacterial and fungal microbiota of total mixed ration silage stored at various temperatures – Wali et al. – Journal of Applied Microbiology

Bioinformatics

Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community – Lyalina – PLOS One

Techniques

THOR’s Hammer: the Antibiotic Koreenceine Drives Gene Expression in a Model Microbial Community – Hurley et al. – mBio

Microbes in the news

Bacteria generate electricity from methane

April 6, 2022

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Today’s digest features studies on microbial genes of unknown function, oral microbiome of smokeless tobacco consumers, non-industrialized infant microbiome, and more news. Happy reading!

Microbiome Forum FOR EVERYONE
Each event is replicated shortly thereafter to reach a global audience.
ALL microbiome research & career levels welcome!
Free registration.

Global microbiome

Global Distribution of mcr Gene Variants in 214K Metagenomic Samples – Hannah-Marie Martiny – mSystems

Symposium Review: After the storm—Perspectives on the taxonomy of Lactobacillaceae – Nanzhen Qiao – JDS Communications

Oral microbiome

Assessing the Effect of Smokeless Tobacco Consumption on Oral Microbiome in Healthy and Oral Cancer Patients – Rituja Saxena – Frontiers in Cellular and Infection Microbiology

Gut microbiome

Unravelling specific diet and gut microbial contributions to inflammatory bowel disease – Gabriel Vasconcelos Pereira – bioRxiv

Effects of caloric restriction on the gut microbiome are linked with immune senescence – Julia Sbierski-Kind – Microbiome

Tap water as a natural vehicle for microorganisms shaping the human gut microbiome – Gabriele Andrea Lugli – Environmental Microbiology

Review: Diet-gut microbiota interactions on cardiovascular disease – Xufei Zhang and Philippe Gérard – Computational and Structural Biotechnology Journal

*Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles – Matthew R Olm – bioRxiv

Animal microbiome

Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance – Yunyan Zhou – Microbiome

Animal experiment

Modulation of the gut microbiome by novel synthetic glycans for the production of propionate and the reduction of cardiometabolic risk factors – Yves A Millet – bioRxiv

Plant microbiome

The phyllosphere microbiome shifts toward combating melanose pathogen – Pu-Dong Li – Microbiome

Wastewater microbiome

Near-neutral pH increased n-caprylate production in a microbiome with product inhibition of methanogenesis – Rodolfo Palomo-Briones – bioRxiv

Techniques

Review: Next-generation sequencing: insights to advance clinical investigations of the microbiome – Caroline R. Wensel – The Journal of Clinical Investigations

Metagenomics-enabled microbial surveillance – Karrie K. K. Ko – Nature Microbiology

Bioinformatics

Software testing in microbial bioinformatics: a call to action – Boas C.L. van der Putten – Microbial Genomics

Review: Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation – Alban Mathieu – Frontiers in Microbiology

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

NSURP is a community-driven initiative to create rewarding remote summer research opportunities for BIPOC and Latinx undergraduate students in the Microbiology, Immunology, and Cancer Biology Sciences.

July 16, 2021

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Today’s digest features studies on environmental contamination of carbapenem-resistant Klebsiella pneumoniae in China (spoiler: extensive contamination, but has negligible impact on patient colonisation), the dynamic change and correlation of microbiome from different body sites to the treatment response as well as immune-related adverse events of immunotherapy in lung cancer patients, and more.

Also, check out a regularly-updated collection of FREE, ONLINE microbiome events. Happy Friday!

Human microbiome

*Prospective correlation between the patient microbiome with response to and development of immune-mediated adverse effects to immunotherapy in lung cancer – Justin Chau – BMC Cancer

Gut microbiome

Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner – Emmanuel Montassier – Nature Microbiology

Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects – Sandeep Verma – PlosOne

Differences in the individual curative effect of acupuncture for obese women with polycystic ovary syndrome based on metagenomic analysis: study protocol for a randomized controlled trial – Huaying Fan – Trials

Comparative Analysis of 16S rRNA Gene and Metagenome Sequencing in Pediatric Gut Microbiomes – Danielle Peterson – Frontiers in Microbiology

Resistome

*Spread of Carbapenem-Resistant Klebsiella pneumoniae in an Intensive Care Unit: A Whole-Genome Sequence-Based Prospective Observational Study – Li Wei – Microbiology Spectrum

*Linezolid- and multidrug-resistant enterococci in raw commercial dog food, Europe, 2019–2020 – Ana R. Freitas – Emerging Infectious Diseases

Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study – Huan Chen – PeerJ

Predicting antibiotic resistance gene abundance in activated sludge using shotgun metagenomics and machine learning – Yuepeng Sun – Water Research

Animal microbiome

Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers – Déborah Romaskevis Gomes Lopes – Journal of Animal Science and Biotechnology

Animal experiment

An osmotic laxative renders mice susceptible to prolonged Clostridioides difficile colonization and hinders clearance – Sarah Tomkovich – bioRxiv

Bioinformatics

Critical Assessment of Metagenome Interpretation – the second round of challenges – F. Meyer – bioRxiv

Disentangling environmental effects in microbial association networks – Maria Deutschmann – bioRxiv

Webinars &c

Microbiome Virtual International Conference #MVIF – September 14

June 25, 2021

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This week, the microbial sciences community worldwide (virtually) united at the World Microbe Forum – meeting highlights you can find here #WorldMicrobeForum.

Today’s digest features studies on group B Streptococcus pathogenesis, dental microbiota and aGVHD Risk, a book about writing and publishing papers, and more. Also, check out a collection of FREE, ONLINE microbiome events. Happy Friday!

Read about the experiences of 338 early career researchers from 36 countries with their mentors in Mentorship in life sciences: voices of mentees by A. Murat Eren (Meren)!

General microbiome

Behind the paper: Describing and naming bacteria in the 21st century – Thomas Hitch – Nature blog

Hierarchical control of microbial community assembly – Sammy Pontrelli – bioRxiv

Resistome

*L-form switching confers antibiotic, phage and stress tolerance in pathogenic Escherichia coli – Aleksandra Petrovic Fabijan – bioRxiv

Gut microbiome

A newly identified protein from Akkermansia muciniphila stimulates GLP-1 secretion – Patrice D. Cani and Claude Knauf – Cell Metabolism

Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics – Anna Pryszlak – arXiv

Dispersal strategies shape persistence and evolution of human gut bacteria – Falk Hildebrand – Cell Host & Microbe

Urinary microbiome

Review: Urinary Microbiome: Yin and Yang of the Urinary Tract – Virginia Perez-Carrasco – Frontiers in Cellular and Infection Microbiology

Vaginal microbiome

Cysteine dependence in Lactobacillus iners constitutes a novel therapeutic target to modify the vaginal microbiota – Seth M. Bloom – bioRxiv

*A type VII secretion system in Group B Streptococcus mediates cytotoxicity and virulence – Brady L Spencer – bioRxiv

Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omics – Zhuye Jie – Genomics, Proteomics & Bioinformatics

Predictive functional analysis reveals inferred features unique to cervicovaginal microbiota of African women with bacterial vaginosis and high-risk human papillomavirus infection – Harris Onywera – PlosOne

Effect of metronidazole on vaginal microbiota associated with asymptomatic bacterial vaginosis – Daniel Ruiz-Perez – Access Microbiology

Oral microbiome

*Dental Biofilm Microbiota Dysbiosis Is Associated With the Risk of Acute Graft-Versus-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation – Vitor Heidrich – Frontiers in Immunology

Fusobacterium nucleatum metabolically integrates commensals and pathogens in oral biofilms – Akito Sakanaka – bioRxiv

Animal microbiome

*Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches – Sharon A. Huws – Microbiome

Animal experiments

A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes – Marion Darnaud – bioRxiv

Bioinformatics

GUNC: detection of chimerism and contamination in prokaryotic genomes – Askarbek Orakov – BMC Genome Biology

metaMIC: reference-free Misassembly Identification and Correction of de novo metagenomic assemblies – Senying Lai – bioRxiv

Open challenges for microbial network construction and analysis – Karoline Faust – The ISME Journal 2021

STRipy: a graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data – Andreas Halman – bioRxiv

Adapting macroecology to microbiology: using occupancy modelling to assess functional profiles across metagenomes – Angus S Hilts – bioRxiv

Webinars &c

Microbiome Virtual International Conference #MVIF – September 14

The International Conference on Group B Strep (ICGBS) – July 20-22

World Enterococcus Day – July 15 – Registration here

BiATA2021 Bioinformatics: from Algorithms to Applications – July 12–15 


LSfM Lecture Series & Workshops : “The Dark Side of Science: Misconduct in Biomedical Research” Dr. Elisabeth Bik – more info here – June 30

EMBARK Webinars – Kimberly Kline “Pathogenesis and persistence during Enterococcus faecalis biofilm-associated infection” and Sofia Forslund “High-throughput measurement of host and microbiota” – EMBARK project – June 30

Writing

Writing and Publishing Scientific Papers: A Primer for the Non-English Speaker – Gábor Lövei – OpenBook Publishers

Art

From Scientist to SciArtist – Eliza Wolfson


April 23, 2021

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Good morning from New Jersey! Lots of papers to share today, particularly regarding animal microbiota and new bioinformatics tools.

General microbiome

Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer, Alice Tzeng et al., Genome Medicine

Pregnancy and early life

The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition, Xuanji Li et al., Cell Host & Microbe

Multi-site human microbiome

Review: Microbiome-immune interactions in tuberculosis, Giorgia Mori et al., PLOS Pathogens

Human gut microbiome

Dynamic Changes in Microbiome Composition Following Mare’s Milk Intake for Prevention of Collateral Antibiotic Effect, Almagul Kushugulova et al., Frontiers in Cellular and Infection Microbiology

Review: The aging gut microbiome and its impact on host immunity, Bosco and Noti, Genes & Immunity

Animal experiments

Ingestion of Bifidobacterium longum changes miRNA levels in the brains of mice, DeVries and Horstman et al., PLOS ONE

Heat-inactivated Lactobacillus plantarum nF1 promotes intestinal health in Loperamide-induced constipation rats, Seon-Ah Park et al., PLOS ONE

The pregnane X receptor drives sexually dimorphic hepatic changes in lipid and xenobiotic metabolism in response to gut microbiota in mice, Sharon Ann Barretto et al., Microbiome

One dog’s waste is another dog’s wealth: A pilot study of fecal microbiota transplantation in dogs with acute hemorrhagic diarrhea syndrome, Arnon Gal et al., PLOS ONE

Animal microbiome

Diversity and functional landscapes in the microbiota of animals in the wild, Levin, Raab, Pinto, and Rothschild et al., Science

Microbiome reduction and endosymbiont gain from a switch in sea urchin life history, Tyler J. Carrier et al., PNAS

Diet and gut microbiome enterotype are associated at the population level in African buffalo, Claire E. Couch et al., Nature Communications

Coral microbiome changes over the day–night cycle, Alicia M. Caughman et al., Coral Reefs

An investigation of conventional microbial culture for the Naja atra bite wound, and the comparison between culture-based 16S Sanger sequencing and 16S metagenomics of the snake oropharyngeal bacterial microbiota, Mao and Chuang et al., PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Preprint: Genome-centric analyses of seasonal phyllosphere microbiome activities in perennial crops, Adina Howe et al., bioRxiv

Influence of Plant Host and Organ, Management Strategy, and Spore Traits on Microbiome Composition, Kristi Gdanetz et al., Phytobiomes Journal

Built environment

Categorisation of culturable bioaerosols in a fruit juice manufacturing facility, Shirleen M. Theisinger et al., PLOS ONE

Bioinformatics

Preprint: Deconstructing taxa x taxa x environment interactions in the microbiota: A theoretical examination, Senay Yitbarek et al., bioRxiv

Preprint: Extended taxonomic profiling of diverse environments with mOTUs 2.6, Hans-Joachim Ruscheweyh et al., bioRxiv

Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome, Donovan H. Parks et al., Frontiers in Microbiology

Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC, Bruce Parrello et al., PLOS ONE

March 24, 2021

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Human gut microbiome

[OPINION]Targeting the Gut Microbiome to Mitigate Immunotherapy-Induced Colitis in Cancer – Chang et al – Trends in Cancer

Direct impact of commonly used dietary emulsifiers on human gut microbiota – Naimi et al. – Microbiome

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

[REVIEW]Establishing causality in Salmonella-microbiota-host interaction: The use of gnotobiotic mouse models and synthetic microbial communities – Stecher – International Journal of Medical Microbiology

Gut microbiota dysbiosis promotes age-related atrial fibrillation by lipopolysaccharide and glucose-induced activation of NLRP3-inflammasome – Zhang et al. – Cardiovascular Research

Animal microbiome (for animals in the wild)

Composition and structure of the skin microbiota of rorquals off the Eastern South Pacific – Toro et al. – FEMS Microbiology Ecology

Plant, root, and soil microbiome

[PREPRINT]Neural networks and extreme gradient boosting predict multiple thresholds and trajectories of microbial biodiversity responses due to browning – Fontaine et al. – bioRxiv

Comparative microbial antibiotic resistome between urban and deep forest environments – Zheng et al. – Environmental Microbiology Reports

Bioinformatics

[PREPRINT]Genomic characterization of three novel Desulfobacterota classes expand the metabolic and phylogenetic diversity of the Phylum – Murphy et al. – bioRxiv

March 12, 2021

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Today’s digest is HUGE.

Read about the healthy urogenital microbiome profiling by culturomics, gutSMASH (Specialized Primary Metabolite Analysis From Anaerobic Bacteria), (sub)strains evolution in mice, and AMPSphere (a comprehensive catalog of antimicrobial peptides).

There are interesting results of a new metaanalysis of the neonatal microbiome, maternal strain inheritance, and persistence into adolescence, evaluation of the effect of long-term freezing storage temperature on fecal samples, and estimation of the bioinformatic carbon footprint using the freely available Green Algorithms calculator. Find out more about statistics & challenges in molecular microbiology (with a reproducible research appendix!).

NEWS: The Transbiome project is a community driven research program using crowdfunding and co-creation to discover the diversity of the neo-vaginal microbiome. You can support the project here.

Check out a list of awesome webinars, courses and podcasts. Happy Friday!

Gut microbiome

*A systematic analysis of metabolic pathways in the human gut microbiota – Victòria Pascal Andreu – bioRxiv

*Strain inheritance and neonatal gut microbiota development: A meta-analysis – Daniel Podlesny and W. Florian Fricke – International Journal of Medical Microbiology

Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut – Andrea R. Watson – bioRixv

Effect of fecal microbiota transplantation on neurological restoration in a spinal cord injury mouse model: involvement of brain-gut axis – Yingli Jing – Microbiome

Review: Association between antibiotics and gut microbiome dysbiosis in children: systematic review and meta-analysis – Lucy McDonnell – Gut Microbes

Review: Salmonella versus the Microbiome – Andrew W. L. Rogers – Microbiology and Molecular Biology Reviews

Respiratory microbiome

Strain-Resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis – Marija Dmitrijeva – mBio

Oral microbiome

Review: Resilience of the oral microbiome – William G. Wade – Periodontology 2000

Skin microbiome

Skin microbiota and clinical associations in Netherton sindrome – Veera Sillanpää – JID Innovations

Urogenital microbiome

*Long-term stability of the urogenital microbiota of asymptomatic European women – Magdalena Ksiezarek – BMC Microbiology

Limosilactobacillus urinaemulieris sp. nov. and Limosilactobacillus portuensis sp. nov. isolated from urine of healthy women – Magdalena Ksiezarek – International Journal of Systematic and Evolutionary Microbiology

Vaginal microbiome

The structure and diversity of strain-level variation in vaginal bacteria – Brett A. Tortelli – Microbial Genomics

Obesity is associated with lower bacterial vaginosis prevalence in menopausal but not pre-menopausal women in a retrospective analysis of the Women’s Interagency HIV Study – Elizabeth Daubert – PlosOne

Bacterial biofilm formation on vaginal ring pessaries used for pelvic organ prolapse – Felicity G. Gould – International Urogynecology Journal

Animal microbiome

*Long-term storage of feces at −80 °C versus −20 °C is negligible for 16S rRNA amplicon profiling of the equine bacterial microbiome – Stefan Gavriliuc – PeerJ

Differences in the gut microbiomes of dogs and wolves: roles of antibiotics and starch – Yuting Liu – BMC Veterinary Research

An Expanded Gene Catalog of Mouse Gut Metagenomes – Jiahui Zhu – mSphere

Animal experiments

*Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice – Bahtiyar Yilmaz – Cell Host & Microbe

The gut mycobiome of healthy mice is shaped by the environment and correlates with metabolic outcomes in response to diet – Tahliyah S. Mims – Communications Biology

Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments – Hualan Liu – Cell Reports

Tea polyphenols regulate gut microbiota dysbiosis induced by antibiotic in mice – Jie Li – Food Research International

Plant microbiome

Designing a home for beneficial plant microbiomes – Chunxu Song – Current Opinion in Plant Biology

Food

Review: Polymicrobial interaction between Lactobacillus and Saccharomyces cerevisiae: coexistence-relevant mechanisms – Zhenbo Xu – Critical Reviews in Microbiology

Viruses and phages

Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities – Christian Santos-Medellin – The ISME Journal

Review: Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review – Julie Callanan – Microorganisms

Techniques

High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes – Florian Trigodet – bioRxiv

Bioinformatics

*AMPSphere: the worldwide survey of prokaryotic antimicrobial peptides – Célio Dias Santos-Júnior – Zenodo

*A Statistical Perspective on the Challenges in Molecular Microbial Biology – Pratheepa Jeganathan and Susan P. Holmes – arXiv

*The carbon footprint of bioinformatics – Jason Grealey – bioRxiv

*Make Interactive Complex Heatmaps in R – Zuguang Gu and Daniel Huebschmann – bioRxiv

Machine learning applications in microbial ecology, human microbiome studies, and environmental monitoring – Ryan B.Ghannam and Stephen M.Techtmann – Computational and Structural Biotechnology Journal

Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit – Fernando Meyer – Nature Protocols

STATegra: Multi-Omics Data Integration – A Conceptual Scheme With a Bioinformatics Pipeline – Nuria Planell – Frontiers in Genetics

Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences – Grace A. Blackwell – bioRxiv

clinker & clustermap.js: automatic generation of gene cluster comparison figures – Cameron L M Gilchrist & Yit-Heng Chooi – Bioinformatics

gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models – Johannes Zimmermann – Genome Biology

Webinars

mSystems Thinking Series: Diversity, Equity, and Inclusion in Microbiology – ASM – March 26

The Microbiome Centers Consortium Seminar Series – weekly seminars featuring early career researchers – Thursdays

Americas Webinar: Mother’s Milk & Baby’s Bacteria: Discoveries from the CHILD Cohort Study – Meghan Azad – April 14

Courses & Workshops

Get R Done: R Tutorials video series – Chad C. Williams

Machine Learning in Genomics: Tools, Resources, Clinical Applications and Ethics – the NHGRI Genomic Data Science Working Group of the National Advisory Council for Human Genome Research – April 13-14

Podcast

February 2021 Pod: Global Chang‪e‬ – Bengtsson-Palme Lab – Microbiology Lab Pod

Enhancers with Molly Gasperini – Jacob Schreiber – The Bioinformatics Chat

Matthew Schechter: Metagenomics History Part 1 and 2 – Leo Elworth – The Bioinformatics and Beyond Podcast

Ep. 33 Oyster Microbiome with Dr. Rachel Diner – Julie Laurin – Planet B612

Art

UMich Microbial Masterpieces – Community for microbe enthusiasts and artists – Erica Gardner, Anna Urso, Bruna Iunes Sanches
*Check out their giant Winogradsky Panel in the Duderstadt Center gallery

February 25, 2021

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

February 24, 2021

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

General microbiome

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

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

Human microbiome

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

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

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

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

Animal microbiome

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

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

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

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

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

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

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

Functional Foods

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

Water microbiome

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

Techniques

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

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

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

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

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