Category Archives: Animal microbiome

October 16, 2020

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In today’s digest read about how food additives affect the intestinal microbiota and induce intestinal inflammation, the role of the gut microbiome in honey bee nestmate recognition, how to use gene-level analysis to identify microbial “genome islands” associated with human health, and more. Check out the list of audiobooks about microbes. Happy Friday!

General microbiome

Time as a microbial resource – Karen G. Lloyd – Environmental Microbiology Reports

Review: The Central Role of Interbacterial Antagonism in Bacterial Life – S. Brook Peterson – Current Biology

Gut microbiome

*Dietary Emulsifiers Directly Impact Adherent-Invasive E. coli Gene Expression to Drive Chronic Intestinal Inflammation – Emilie Viennois – Cell Reports

Microbial Strain Engraftment, Persistence and Replacement after Fecal Microbiota Transplantation – Daniel Podlesny – medRxiv

Characterization of presumptive vancomycin-resistant enterococci recovered during infection control surveillance in Dallas, Texas – Sara Ping – bioRxiv

Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria – Samir Giri – bioRxiv

Metabolic Response of Faecalibacterium prausnitzii to Cell-Free Supernatants from Lactic Acid Bacteria – Mathilde Lebas – Microorganisms

A combination of metagenomic and cultivation approaches reveals hypermutator phenotypes within Vibrio cholerae infected patients – Inès Levade – bioRxiv

Safety and functional enrichment of gut microbiome in healthy subjects consuming a multi-strain fermented milk product: a randomised controlled trial – Anne-Sophie Alvarez – Scientific Reports

Skin microbiome

Microbial and transcriptional differences elucidate atopic dermatitis heterogeneity across skin sites – Noora Ottman – Allergy

Respiratory microbiome

Multicenter analysis of sputum microbiota in tuberculosis patients – Claudia Sala – PlosOne

Lacticaseibacillus casei AMBR2 modulates the epithelial barrier function and immune response in a donor-derived nasal microbiota manner – Charlotte De Rudder – Scientific Reports

Animal microbiome

*The gut microbiome defines social group membership in honey bee colonies – Cassondra L. Vernier – Science Advances

Early-life gut dysbiosis linked to juvenile mortality in ostriches – Elin Videvall – Microbiome

Animal experiment

The Immune System Fails to Mount a Protective Response to Gram-Positive or Gram-Negative Bacterial Prostatitis – Federico Lupo – Journal of Immunology

The aging mouse microbiome has obesogenic characteristics – Dana Binyamin – Genome Medicine

Tetracycline Antibiotics Induce Host-Dependent Disease Tolerance to Infection – Henrique G. Colaço – Immunity

Water microbiome

Impact of phosphate dosing on the microbial ecology of drinking water distribution systems: Fieldwork studies in chlorinated networks – Isabel Douterelo – Water Research

Sustained nitrogen loss in a symbiotic association of Comammox Nitrospira and Anammox bacteria – Ekaterina Y. Gottshall – bioRxiv

Viruses and phages

Culturing novel and abundant pelagiphages in the ocean – Zefeng Zhang – Environmental Microbiology

High-throughput mapping of the phage resistance landscape in E. coli – Vivek K. Mutalik – PlosBiology

Fungi

Minireview: Fun(gi)omics: Advanced and Diverse Technologies to Explore Emerging Fungal Pathogens and Define Mechanisms of Antifungal Resistance – Brianna Ball – mBio

Technique

Bac-PULCE: Bacterial Strain and AMR Profiling Using Long Reads via CRISPR Enrichment – Andrea Sajuthi – bioRxiv

Bioinformatics

*Gene-level metagenomics identifies genome islands associated with immunotherapy response – Samuel S Minot – bioRxiv

PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom – Keith Mitchell – Frontiers in Microbiology

Raman2imzML converts Raman imaging data into the standard mass spectrometry imaging format – Stefania Alexandra Iakab – BMC Bioinformatics

Scientific writing

Eight problems with literature reviews and how to fix them – Neal R. Haddaway – Nature Ecology & Evolution

Scientific art

Inktober2020 #PathogenPortraits by Dr Eliza Wolfson

Citizen science

The Human Diets & Microbiome Initiative in the US (THDMI): A unique opportunity to become a citizen scientist. Join for FREE to uncover the secret of the gut microbiome.

Books

11 Audiobooks About Microbes – Justine Dees – Joyful Microbe

October 13, 2020

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Today’s mid-week digest is about – meta analysis of metabolic benefits of probiotics, probiotics and synbiotics, microbiome association with narcolepsy type 1, design of microbial consortium for reduced C. difficle colonization, new sequencing technique for pathogen identification in cerebrospinal fluid and many more… Happy reading!

Human microbiome

The effect of probiotics, prebiotics or synbiotics on metabolic outcomes in individuals with diabetes: a systematic review and meta-analysis – Patricia M. Bock – Diabetologia

Effect of a Nonoptimal Cervicovaginal Microbiota and Psychosocial Stress on Recurrent Spontaneous Preterm Birth – Kristin D. Gerson – American Journal of Perinatology

Targeting the microbiome-gut-brain axis for improving cognition in schizophrenia and major mood disorders: A narrative review – Miquel Bioque – Progress in Neuro-Psychopharmacology and Biological Psychiatry

Inflammatory Bowel Disease Environmental Risk Factors: Diet and Gut Microbiota – Sarah Altajar – Current Gastroenterology Reports

Co‐ and polymicrobial infections in the gut mucosa: the host‐microbiota‐pathogen perspective – Teresa Frisan – Cellular Microbiology

Gut microbiota composition is associated with narcolepsy type 1 – Alexandre Lecomte – Neurology

A parental transcriptional response to microsporidia infection induces inherited immunity in offspring – Alexandra R. Willis – BioRxiv

Melamine contamination and associated health risks: Gut microbiota does make a difference – Meenakshi Rajpoot – Biotechnology and Applied Biochemistry

Animal microbiome

Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization – Fátima C. Pereira – Nature Communications

Effects of seasonality and previous logging on faecal helminth-microbiota associations in wild lemurs – I. I. de Winter – Scientific Reports

Bacterial community analysis on the different mucosal immune inductive sites of gastrointestinal tract in Bactrian camels – Wang-Dong Zhang – PlosOne

Sows affect their piglets’ faecal microbiota until fattening but not their Salmonella enterica shedding status – Guillaume Larivière‐Gauthier – Letters in Applied Microbiology

Plant, root and soil microbiome

Comparison of soil microbial community between reseeding grassland and natural grassland in Songnen Meadow – Ruifen Zhu – Scientific Reports

Evidence for signatures of ancient microbial life in paleosols – Katharina Frindte – Scientific Reports

Techniques

Pathogen identification in culture-negative cerebrospinal fluid specimens of patients with purulent meningitis using next-generation sequencing technology – Xin Men – International Journal of Clinical Experimental Pathology

October 09, 2020

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COVID-19
Face masks: what the data say – Lynne Peeples – Nature

Pregnancy and early life

[REVIEW] Can we prevent allergic disease? Understanding the links between the early life microbiome and allergic diseases of childhood – Petersen & Turvey – Current Opinions in Pediatrics

Human skin microbiome

Atopic Dermatitis and the Role of the Skin Microbiome in Choosing Prevention, Treatment, and Maintenance Options – Baldwin ety al. – Journal of Drugs in Dermatology

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

[PREPRINT] Western-style diet impedes colonization and clearance of gut bacterial pathogens – Gewirtz et al. – bioRxiv

Animal microbiome (for animals in the wild)

Taxonomic profiling of individual nematodes isolated from copse soils using deep amplicon sequencing of four distinct regions of the 18S ribosomal RNA gene – Kenmotsu et al. – PLOS One

The red flour beetle Tribolium castaneum: A model for host-microbiome interactions – Agarwal & Agashe – PLOS One

[PREPRINT] Meta-transcriptomic identification of divergent Amnoonviridae in fish – Turnbull et al. – bioRxiv

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

Metagenome analysis from the sediment of river Ganga and Yamuna: In search of beneficial microbiome – Behera et al. – PLOS One

Phages and viruses

[PREPRINT] Thousands of previously unknown phages discovered in whole-community human gut metagenomes – Benler et al. – bioRxiv

Bioinformatics

Metabolic pathway inference using multi-label classification with rich pathway features – Basher, McLaughlin & Hallam – PLOS Computational Biology

Big Data in metagenomics: Apache Spark vs MPI – Abuin et al. – PLOS One

October 07, 2020

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Grant application (US specific grant)
2020 Biocodex Microbiota Foundation US $50,000 grant, supporting cutting edge research on the relationship between gut microbiota and chronic disease.
Deadline: October 15th.
Link: https://www.biocodexmicrobiotafoundation.com/national-call-projects/usa

General microbiome

Understanding the potential of lactobacilli in recurrent UTI prevention – Vagios, Hesham & Mitchel – Microbial Pathogenesis

Throat microbial community structure and functional changes in post-surgery laryngeal carcinoma patients – Hsueh et al. – Applied and Environmental Microbiology

Bacterial diversity and prevalence of antibiotic resistance genes in the oral microbiome – Almeida et al. – PLOS One

Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus – Achtman & Zhou – Philosophical Transactions of the Royal Society B

Pregnancy and early life

In utero human intestine harbors unique metabolomic features including bacterial metabolites – Li et al. – JCI insight

Interactions between Environmental Exposures and the Microbiome: Implications for Fetal Programming – Banerjee, Suter & Aagaard – Current Opinion in Endocrine and Metabolic Research

Human nearly-sterile sites (blood, organs, brain)

Alterations in blood microbiota after colonic cancer surgery – Søby et al. – BJS Open

Human gut microbiome

Estimating molecular preservation of the intestinal microbiome via metagenomic analyses of latrine sediments from two medieval cities – Sabin et al. – Philosophical Transactions of the Royal Society B

Gut microbiota composition in obese and non-obese adult relatives from the highlands of Papua New Guinea – Jonduo et al. – FEMS Microbiology Letters

Fecal Bacteria as Biomarkers for Predicting Food Intake in Healthy Adults – Shinn et al. – The Journal of Nutrition

Animal experiments

Inulin fermentation by lactobacilli and bifidobacteria from dairy calves – Zhu et al. – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Microbial Diversity and Community Structure in Alpine Stream Soil – Rasool et al. – Geomicrobiology Journal

Food microbiology

Impact of dietary fibers in infant formula on gut microbiota and the intestinal immune barrier – Kong et al. – Food & Function

Bioinformatics

[PREPRINT] A framework for comparing microbial networks reveals core associations – Rottjers et al. – bioRxiv

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

Gut health benefits begin in utero – Brita Belli – YaleNews

Medieval poo holds clues to health of modern-day gut microbiome – Sara Rigby – Science Focus

October 6, 2020

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Starting today’s digest with a couple of very interest studies on COVID-19 in Nature and Science. There’s also multiple interesting virome papers today.

COVID-19 & Vaccines

Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans – Mateus et al. Science

The major genetic risk factor for severe COVID-19 is inherited from Neanderthals – Zeberg et al. Nature

Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR – Smyrlaki et al. Nature Communications. 

General microbiome

Identification of new enterosynes using prebiotics: roles of bioactive lipids and mu-opioid receptor signalling in humans and mice – Abot et al. Gut

Assessing the Variation within the Oral Microbiome of Healthy Adults – Nearing et al. mSphere

Strain-Level Analysis of Bifidobacterium spp. from Gut Microbiomes of Adults with Differing Lactase Persistence Genotypes – Schmidt et al. mSystems

Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces – Ghimire et al. PeerJ.

Gut microbiome

Distinct signatures of gut microbiome and metabolites associated with significant fibrosis in non-obese NAFLD – Lee et al. Nature Communications

Animal microbiome 

Fecal microbiota in client-owned obese dogs changes after weight loss with a high-fiber-high-protein diet – Bermudez-Sanchez. PeerJ

Plant microbiome

Achieving similar root microbiota composition in neighbouring plants through airborne signalling – Kong et al. ISME

Phages and viruses

Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization – Zuo et al. Cell Host & Microbe

Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity – Meaden et al. ISME

Interaction of bacterial metagenome and virome in patients with cirrhosis and hepatic encephalopathy – Bajaj et al. Gut

Stability of the Virome in Lab- and Field-Collected Aedes albopictus Mosquitoes across Different Developmental Stages and Possible Core Viruses in the Publicly Available Virome Data of Aedes Mosquitoes – Shi et al. mSystems

October 2, 2020

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Today’s exciting updates – FMT method to restore normal microbial development in caesarean-born infants, mechanism unveiled how dietary tryptophan improves alcohol induced liver injury, advance in droplet based microfluidics to study host-microbiome interactions, prebiotics encapsulation of probiotic to suppress colon cancer and new hope to curb plastic waste by discovery of plastic-eating enzyme cocktail. Happy weekend, stay safe!

General microbiome

Eligible blood donors’ decisions about donating stool for fecal microbiota transplantation: Does ambivalence play a role? – Melissa K. Hyde – Transfusion

Microbiota-Dependent Effects of IL-22 – Morsal Sabihi – Cells

Human microbiome

Maternal Fecal Microbiota Transplantation in Cesarean-Born Infants Rapidly Restores Normal Gut Microbial Development: A Proof-of-Concept Study – Katri Korpela – Cell

Comparative analysis of the tonsillar microbiota in IgA nephropathy and other glomerular diseases – Ji In Park – Scientific Reports

Dysbiosis in the oral microbiomes of anti-CCP positive individuals at risk of developing rheumatoid arthritis – Zijian Cheng – Annals of the Rheumatic Diseases

Animal microbiome

Microbiota tryptophan metabolism induces aryl hydrocarbon receptor activation and improves alcohol-induced liver injury – Laura Wrzosek – Gut

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients – Alfonsina D’Amato – Microbiome

Competitive reduction of poultry-borne enteric bacterial pathogens in chicken gut with bioactive Lactobacillus casei – Zajeba Tabashsum – Scientific Reports

Offspring susceptibility to metabolic alterations due to maternal high-fat diet and the impact of inhaled ozone used as a stressor – Samantha J. Snow – Scientific Reports

Beneficial effects of mung bean seed coat on the prevention of high-fat diet-induced obesity and the modulation of gut microbiota in mice – Dianzhi Hou – European Journal of Nutrition

Prebiotics‐Encapsulated Probiotic Spores Regulate Gut Microbiota and Suppress Colon Cancer – Di‐Wei Zheng – Advanced Materials

Multi-Omic Analysis Reveals Different Effects of Sulforaphane on the Microbiome and Metabolome in Old Compared to Young Mice – Se-Ran Jun – Microorganisms

Plant microbiome

Protists as catalyzers of microbial litter breakdown and carbon cycling at different temperature regimes – Stefan Geisen – Isme Journal

Techniques

Investigating host-microbiome interactions by droplet based microfluidics – Alexandra S. Tauzin – Microbiome

Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis – Sidney P. Walker – Scientific Reports

Non-microbiology picks

Plastic-eating enzyme ‘cocktail’ heralds new hope for plastic waste – Science Daily

October 1, 2020

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Greetings, friends!

Today’s digest contains a wealth of microbiology articles focused on everything from the dog ear canal microbiome to estuarine methanogen communities. Rather than highlight a specific research article, today I’d like to encourage you to check out this week’s New York Times article profiling the organizers of Black in Micro Week and this commentary published by one of the organizers in mSphere. Black in Micro week began this Monday and programming is scheduled to continue through October 4th. If you missed earlier events, you’re in luck! The organizers have already uploaded videos of all completed events at the Black in Micro youtube channel.

Enjoy!

Events

Black in Micro Week is this week (September 28 – October 4th, 2020) on your favorite social media platforms! Check out the Black in Microbiology website for additional information, including a full programming schedule, and follow @BlackinMicro and #BlackinMicro on Twitter and Instagram.

Human respiratory microbiome

Airway microbiota is associated with the severity of non‐CF bronchiectasis – Li et al. – The Clinical Respiratory Journal

Human gut microbiome

Systematic analysis of gut microbiota in pregnant women and its correlations with individual heterogeneity – Yang et al. – npj Biofilms and Microbiomes

Review: Implication of gut microbiota in cardiovascular diseases – Zhou et al. – Oxidative Medicine and Cellular Longevity

Animal experiments

Changes in the ear canal microbiota of dogs with otitis externa – Kasai et al. – Journal of Applied Microbiology

Plant, root, and soil microbiome

Soil borne Fusarium solani exhibited pathogenic effect on tomato cultivars in Nigeria – Abiala et al. – Archives of Phytopatholgy and Plant Protection

A symbiotic nutrient exchange within the cyanosphere microbiome of the biocrust cyanobacterium, Microcoleus vaginatus – Nelson et al. – The ISME Journal

Successional change of the fungal microbiome pine seedling roots inoculated with Tricholoma matsutake – Park et al. – Frontiers in Microbiology

Review: Arbuscular mycorrhizal fungi: an ecological accelerator of phytoremediation of metal contaminated soils – Tiwari et al. – Archives of Agronomy and Soil Science

Co‐occurrence history increases ecosystem stability and resilience in experimental plant communities – van Moorsel et al. – Ecology

Quantitative estimation of stochastic and deterministic processes for soil prokaryotic community assembly in the Yellow River floodplain – Yu et al. – European Journal of Soil Science

Water and extremophile microbiome

Homogeneous environmental selection dominates microbial community assembly in the oligotrophic South Pacific Gyre – Allen et al. – Molecular Ecology

An unexpectedly broad thermal and salinity-tolerant estuarine methanogen community – Blake et al. – Microorganisms

Microbial communities responded to tetracyclines and Cu(II) in constructed wetlands microcosms with Myriophyllum aquaticum – Guo et al. – Ecotoxicology and Environmental Safety

Built environment

Microbial community and function in nitrogen transformation of ectopic fermentation bed system for pig manure composting – Chen et al. – Bioresource Technology

Effect of hydrothermal hot-compression method on the antimicrobial performance of green building materials from heterogeneous cellulose wastes – Echeverria et al. – Journal of Cleaner Production

Nitrous oxide emission and microbial community of full-scale anoxic/aerobic membrane bioreactors at low dissolved oxygen setpoints – Wen et al. – Journal of Water Process Engineering

Response of Cyperus involucratus to sulfamethoxazole and ofloxacin-contaminated environments: Growth physiology, transportation, and microbial community – Xu et al. – Ecotoxicology and Environmental Safety

Microbes in the news

Black microbiologists push for visibility amid a pandemic – Wu – New York Times

Science, publishing, and career

Commentary: mSphere of influence: That’s racist—COVID-19, biological determinism, and the limits of hypotheses – Taylor – mSphere

September 28, 2020

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In today’s digest read about ureteral stent microbiota, metagenomic growth estimators, social transmission as a major shaper of gut microbiota in wild mice [spoiler: mice with many friends in separate social circles have the richest microbiota], and give a listen to the first episode of Lonely Pipette, a brand new podcast about doing better science!

General microbiome

Review: Searching for principles of microbial physiology – Frank J Bruggeman – FEMS Microbiology Reviews

Metagenomics

*Benchmarking microbial growth rate predictions from metagenomes – Andrew M. Long – The ISME Journal

Metabolomics

Review: Gut microbial metabolites as multi-kingdom intermediates – Kimberly A. Krautkramer – Nature Reviews Microbiology

Multi-omics

Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes – Francesco Delogu – Nature
Behind the paper: What can absolute multi-omics add to microbial ecology?

Gut microbiome

Macrophages Maintain Epithelium Integrity by Limiting Fungal Product Absorption – Aleksandra S. Chikina – Cell

Review: Anorexia nervosa and gut microbiota: A systematic review and quantitative synthesis of pooled microbiological data – Laura Di Lodovico – Progress in Neuro-Psychopharmacology and Biological Psychiatry

In search for interplay between stool microRNAs, microbiota and short chain fatty acids in Crohn’s disease – a preliminary study – Filip Ambrozkiewicz – BMC Gastroenterology

Vaginal microbiome

Slipped strand mispairing in the gene encoding cell wall associated sialidase NanH3 in Gardnerella spp – Shakya P. Kurukulasuriya – bioRxiv

The vaginal microbiome in pregnant women: knowledge gaps in relation to clinical relevance – Steven S. Witkin – BJOG: An International Journal of Obstetrics and Gynaecology

Urinary microbiome

*Ureteral Stent Microbiota Is Associated with Patient Comorbidities but Not Antibiotic Exposure – Kait F. Al – Cell Reports Medicine

Novel Antibiotic-Loaded Particles Conferring Eradication of Deep Tissue Bacterial Reservoirs for the Treatment of Chronic Urinary Tract Infection – Wai Lau – Journal of Controlled Release

Respiratory microbiome

Altered respiratory microbiota composition and functionality associated with asthma early in life – Mohammad T. AL Bataineh – BMC Infectious Diseases

Oral microbiome

Comparative evaluation of microbial profiles of oral samples obtained at different collection time points and using different methods – Michi Omori – Clinical Oral Investigations

Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment – Xiaoyu Sun – Scientific Reports

Animal microbiome

Habitat disturbance influences the skin microbiome of a rediscovered neotropical-montane frog – Randall R. Jiménez – BMC Microbiology

Lactobacillus spp. attenuate antibiotic-induced immune and microbiota dysregulation in honey bees – Brendan A. Daisley – Communications Biology

Animal experiment

Antibiotics increase aggression behavior and aggression-related pheromones and receptors in Drosophila melanogaster – Michal Grinberg – bioRxiv

*Social networks strongly predict the gut microbiota of wild mice – Aura Raulo – bioRxiv

Plant/root/soil microbiome

Insights into the diversity and survival strategies of soil bacterial isolates from the Atacama Desert – Alicyn Reverdy – bioRxiv

Rhizobacterial species richness improves sorghum growth and soil nutrient synergism in a nutrient-poor greenhouse soil – Mohammad Radhi Sahib – Scientific Reports

Water microbiome

Bacterial Opportunistic Pathogen Gene Markers in Municipal Drinking Water are Associated with Distribution System and Household Plumbing Characteristics – Sarah Haig – Environmental Science: Water Research & Technology

Collection system investigation microbial source tracking (CSI-MST): Applying molecular markers to identify sewer infrastructure failures – Dana Gonzalez – Journal of Microbiological Methods

New insights into the vertical distribution and microbial degradation of microplastics in urban river sediments – Lihua Niu – Water Research

Unveiling dynamics of size-dependent antibiotic resistome associated with microbial communities in full-scale wastewater treatment plants – Kaifeng Yu – Water Research

Aerobic microbial communities in the sediments of a marine oxygen minimum zone – Sabyasachi Bhattacharya – FEMS Microbiology Letters

Phages and viruses

Identification of Bacteriophages in the Vagina of Pregnant Women: A Descriptive Study – Antonio Charlys da Costa – BJOG: An International Journal of Obstetrics and Gynaecology

The Protective Effect of Staphylococcus epidermidis Biofilm Matrix against Phage Predation – Luís D.R. Melo – Viruses

Bioinformatics

Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation – Dileep Kishore – bioRxiv

GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure – Yu Wan – BMC Genomics

A network approach to elucidate and prioritize microbial dark matter in microbial communities – Tatyana Zamkovaya – The ISME Journal

Podcast

*TLP #1: Navigating the path to team leader, guest: Maxim Greenberg – Renaud Pourpre and Jonathan Weitzman – The Lonely Pipette: helping scientists do better science

Burnout Syndrome, guest: Beth Thompson – Christine Boinett – Your Digital Mentor Podcast

August 2020 Pod: From the deep sea to the lost sense of smell – Bengtsson-Palme Lab – Microbiology Lab Pod

Events &c

Black In Microbiology Week [September 28 – October 4]
a vibrant celebration of Black microbiologists, with talks & panels featuring microbiologists across career stages and subdisciplines

How CHROMagar™ Revolutionized Microbe Identification – Andrea Prinzi – ASM
*Submit a Masterpiece to ASM Agar Art 2020!

The National Summer Undergraduate Research Project (NSURP) #nolabnoproblem initiative – Projects & Presentations

September 25, 2020

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Hello from Lübeck/Germany,
today we cover a broad range of microbiome related studies. Of particular interest is a preprint by the Korem lab about use of antibiotics and increase in aggressive behavior in D. melanogaster. This study got already some attention on Twitter and in the press. Furthermore, one preprint covers the C. difficile species problem, investigating the genetic heterogeneity of this species. Last but not least, I would like to mention a paper investigating responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories.

COVID-19

[PREPRINT] Longitudinal multi-omics analysis identifies responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories – Bernardes et al. – medRxiv

General microbiome

[PREPRINT] The Clostridioides difficile species problem: global phylogenomic analysis uncovers three ancient, toxigenic, genomospecies – Knight et al. – bioRxiv

Human respiratory microbiome

Longitudinal Changes in Early Nasal Microbiota and the Risk of Childhood Asthma – Toivonen et al. – Pediatrics

Human gut microbiome

[REVIEW] Host–microbiota maladaptation in colorectal cancer – Janney, Pworie & Mann – Nature

Animal experiments

The maternal microbiome modulates fetal neurodevelopment in mice – Vuong et al. – Nature

[PREPRINT] Antibiotics increase aggression behavior and aggression-related pheromones and receptors in Drosophila melanogaster – Grinberg et al. – bioRxiv

Plant, root, and soil microbiome

[PREPRINT] Viruses carrying genes for microbial extremotolerance are abundant and widely dispersed in the Atacama Desert hyperarid soil – Hwang et al. – bioRxiv

Water and extremophile microbiome

[PREPRINT] Enrichment of novel Verrucomicrobia, Bacteroidetes and Krumholzibacteria in an oxygen-limited, methane- and iron-fed bioreactor inoculated with Bothnian Sea sediments – Martins et al. – bioRxiv

Built environment

[PREPRINT] The rise and the fall of a Pseudomonas aeruginosa epidemic lineage in a hospital – Petitjean et al. – bioRxiv

Metabolic traits

Metabolic trait diversity shapes marine biogeography – Deutsch, Penn & Seibel – Nature

Bioinformatics

[Preprint] Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation – Kishore et al. – bioRxiv

Microbes in the news

Tiny bacteria impact our health in big ways – Gina Rich – The Washington Post (KidsPost)

Gut microbiome plays important role in sleep regulation – ScienceDaily

September 23, 2020

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General microbiome
Chemotaxis under flow disorder shapes microbial dispersion in porous media – Pietro de Anna – Nature Physics

REVIEW: A piece of the pie: engineering microbiomes by exploiting division of labor in complex polysaccharide consumption – Stephen RLindemann – Current Opinion in Chemical Engineering

Benchmarking microbial growth rate predictions from metagenomes – Andrew M. Long – The ISME Journal

Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes – F. Delogu – Nature Communications

Spatial Variance of Species Distribution Predicts the Interspecies Interactions within a Microbial Metacommunity – So-Yeon Jeong & Tae Gwan Kim – Microbial Ecology

Human microbiome
The Social Distancing Imposed To Contain COVID-19 Can Affect Our Microbiome: a Double-Edged Sword in Human Health – Célia P. F. Domingues – mSphere

Gut microbiome
Auto-reactivity against gut bacterial peptides in patients with late-onset diabetes – Mohammad Sajid – Autoimmunity

REVIEW: The gut microbiome in pediatric patients undergoing allogeneic hematopoietic stem cell transplantation – Riccardo Masetti – Pediatric Blood & Cancer

Gut Microbiota and Metabolome Alterations Associated with Parkinson’s Disease – Sarah Vascellari – mSystems

REVIEW: Gut Microbiota Resilience: Definition, Link to Health and Strategies for Intervention – Shaillay Kumar Dogra – Frontiers in Microbiology

Deciphering the impact of diet and host physiology on the mammalian gut microbiome by multi-omics approaches – Christian Milani – Applied and Environmental Microbiology

Oral microbiome
High altitude as a possible factor for dysbiosis of salivary microbiome in orthodontic patients – Ibrahim AlShahrani – Archives of Oral Biology

Pregnancy and early life microbiome
Changes in Gut Microorganism in Patients with Positive Immune Antibody-Associated Recurrent Abortion – Min Jin – BioMed Research International

Contrasting microbiota profiles observed in children carrying either Blastocystis spp. or the commensal amoebas Entamoeba coli or Endolimax nana – Juan F. Alzate – Scientific Reports

Biological observations in microbiota analysis are robust to the choice of 16S rRNA gene sequencing processing algorithm: case study on human milk microbiota – Shirin Moossavi – BMC Microbiology

Microbiome of near sterile sites
Metagenome analysis using serum extracellular vesicles identified distinct microbiota in asthmatics – Ji-Hyang Lee – Scientific Reports

Lung microbiome
REVIEW: Reconsidering ventilator-associated pneumonia from a new dimension of the lung microbiome – Laia Fernández-Barata – EBioMedicine

Animal microbiome
The impact of anthelmintic treatment on gut bacterial and fungal communities in diagnosed parasite-free sika deer Cervus nippon – Xiaolong Hu – Applied Microbiology and Biotechnology

Host phylogeny and life history stage shape the gut microbiome in dwarf (Kogia sima) and pygmy (Kogia breviceps) sperm whales – Elizabeth R. Denison – Scientific Reports

Animal experiment
Altered gut microbiome accompanying with placenta barrier dysfunction programs pregnant complications in mice caused by graphene oxide – Xiaojing Liu – Ecotoxicology and Environmental Safety

Comparative analysis of the pulmonary microbiome in healthy and diseased pigs – Zongjie Li – Molecular Genetics and Genomics

Diet posttranslationally modifies the mouse gut microbial proteome to modulate renal function – Lior Lobel – Science

Plant, root, and soil microbiome
REVIEW: Overhauling the assessment of agrochemical-driven interferences with microbial communities for improved global ecosystem integrity – Mengcen Wang & Tomislav Cernava – Environmental Science and Ecotechnology

Susceptibility and resilience of the soil ciliate community to high temperatures – Takaaki Oshima – Soil Science and Plant Nutrition

Food microbiology
Novel approaches for the identification of microbial communities in kimchi: MALDI-TOF MS analysis and high-throughput sequencing – Eiseul Kim – Food Microbiology

Water microbiome
The Nutrient Removal Ability and Microbial Communities in a Pilot-Scale Horizontal Subsurface Flow Constructed Wetland Fed by Slightly Polluted Lake Water – Weigang Wang – Wetland

Pre-print
Impact of temporal pH fluctuations on the coexistence of nasal bacteria – Sandra Dedrick – bioRxiv

Study of growth, metabolism, and morphology of Akkermansia muciniphila with an in vitro advanced bionic intestinal reactor – Xiaobei Zhan – bioRxiv