December 31, 2020

General microbiome

Review: Brain-gut axis: From the conditioned reflex to the microbiota-gut-brain communication system – Klara Gyires – Integrative Physiology

Human skin microbiome

Microbiological profile of diabetic foot ulcers in Kuwait – Asma Alhubail – PLOS ONE

Human respiratory microbiome

The airways microbiome of individuals with asthma treated with high and low doses of inhaled corticosteroids – Matthew J Martin – PLOS ONE

Human gut microbiome

The beneficial or detrimental fluoride to gut microbiota depends on its dosages – Guijie Chen – Ecotoxicology and Environmental Safety

Review: Synthetic Gut Microbiome: Advances and Challenges – Humphrey A. Mabwi – Computational and Structural Biotechnology Journal

Review: Microbiota-Gut-Brain Axis as a Regulator of Reward Process – Rubén García-Cabrerizo – Journal of Neurochemistry

Review: Modulatory effects of gut microbiome in cancer immunotherapy: A novel paradigm for blockade of immune checkpoint inhibitors – Sama Rezasoltani – Cancer Medicine

Animal experiments

Effects of heat-killed Enterococcus faecalis T-110 supplementation on gut immunity, gut flora, and intestinal infection in naturally aged hamsters – Takio Inatomi – PLOS ONE

Nasal Tissue Extraction Is Essential for Characterization of the Murine Upper Respiratory Tract Microbiota – L Patrick Schenck – mSphere

Animal microbiome

Review: Gut microbiota of animals living in polluted environments are a potential resource of anticancer molecules – Morhanavallee Soopramanien – Journal of Applied Microbiology

Plant, root, and soil microbiome

Metabarcoding on both environmental DNA and RNA highlights differences between fungal communities sampled in different habitats  – Martino Adamo – PLOS ONE

Changes in microbial communities at different soil depths through the first rainy season following severe wildfire in North China artificial Pinus tabulaeformis forest – Qianqian Qin – Journal of Environment Management

Shifts in a Phenanthrene-Degrading Microbial Community are Driven by Carbohydrate Metabolism Selection in a Ryegrass Rhizosphere – Longfei Jiang – ACS

Forest gaps mediate the structure and function of the soil microbial community in a Castanopsis kawakamii forest – Xuelin Wang – Ecological Indicators

Review: Herbicide bioremediation: from strains to bacterial communities – Marcos Pileggi – Heliyon

Spatial scale structure soil bacterial communities across an Arctic landscape – Lucie A Malard – Applied and Environmental Microbiology

Metagenomic Analysis of Rhizosphere Bacteria in Desert Plant Calotropis procera – Ahmed M Ramadan

Water and extremophile microbiome

Archaeal communities of low and high microbial abundance sponges inhabiting the remote western Indian Ocean island of Mayotte – Ana Rita Moura Polónia – Antonie van Leeuwenhoek

Preprint: Novel integrative elements and genomic plasticity in ocean ecosystems – Thomas Hackl – bioRxiv

Food microbiology

The diversity of microbial communities in Chinese milk fan and their effects on volatile organic compound profiles – Chen Chen – Journal of Dairy Science

Characterizing Relationship of Microbial Community in Xiaoqu and Volatiles of Light-aroma-type Xiaoqu Baijiu – Zhe Wang – Food Science and Technology Research

Virus and phages

Acquisition, prevalence and clearance of type-specific human papillomavirus infections in young sexually active Indian women: A community-based multicentric cohort study – Richard Muwonge – PLOS ONE

Techniques

Informed sequential pooling approach to detect SARS-CoV-2 infection – Renato Millioni – PLOS ONE

Thesis: Statistical Methods for Longitudinal Data Analysis and Reproducible Feature Selection in – Lingjing Jiang – UC San Diego Electronic Theses and Dissertations

MicroGMT: A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences – Yue Xing – Frontiers in Microbiology

Microbes and evolution

Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history – Eva Brons – PLOS BIOLOGY

The role of Ulva fasciata in the evolution of the microbial community and antibiotic resistance genes in maricultural sediments – Yuqin Luo – Marine Pollution Bulletin

Preprint: The Diversity and Evolution of Microbial Dissimilatory Phosphite Oxidation – Sophia D Ewens – bioRxiv

Microbes in the news

Synthetic Biologics Inc. (SYN) Soars 5.43% on December 25 – equities.com

The Brain, Gut and Consciousness: Microbiology of Our Mind – Inquiries Journal

Non-microbiology pick

Preprint: National Institutes of Health Institute and Center Award Rates and Funding Disparities – Michael S Lauer – bioRxiv

Communicating risk in human-wildlife interactions: How stories and images move minds – Sarah K Guenther – PLOS ONE

December 16, 2020

COVID19

Inferring the effectiveness of government interventions against COVID-19 – Brauner et al. – Science

COVID 19 mortality: Probable role of microbiome to explain disparity – Kumar & Chander – Medical Hyptheses

General microbiome

[PREPRINT] Theory of (antimicrobial) relativity: When competitors determine a species’ drug sensitivity. – Reding – bioRxiv

Human respiratory microbiome

Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients – Mostafa et al. – mBio

Human oral microbiome

Variation in oral microbiome is associated with future risk of lung cancer among never-smokers – Hosgood et al. – Lung cancer

Human gut microbiome

Effect of an 8-week Exercise Training on Gut Microbiota in Physically Inactive Older Women – Zhong et al. – Int J Sports Med

Vitamin D metabolites and the gut microbiome in older men – Thomas et al. – Nature Communications

Animal microbiome

[PREPRINT] Longitudinal profiling of the macaque vaginal microbiome reveals similarities to diverse human vaginal communities: implications for use as a pre-clinical model for bacterial vaginosis – Rhoades et al. – bioRxiv

The earthworm microbiome is resilient to exposure to biocidal metal nanoparticles – Swart et al. – Environmental Pollution

Plant, root, and soil microbiome

Environmental microbiome mapping as a strategy to improve quality and safety in the food industry – Filippis et al. – Current Opinion in Food Science

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

Nitrosophilus alvini gen. nov., sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the East Pacific Rise, inferred by a genome-based taxonomy of the phylum “Campylobacterota” – Shiotani et al. – PLOS One

Techniques

A rapid approach to profiling diverse fungal communities using the MinION™ nanopore sequencer – Mafune et al. – BioTechniques

[PREPRINT] Microbe-seq: high-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome – Zheng et al. – bioRxiv

Microbes in the news

Oral Microbiome Diversity and Species Abundance Linked to Lung Cancer in Nonsmokers

November 26, 2020

Greetings from Pittsburgh!

Today’s digest is heavy on environmental microbiology work, especially plant, root, and soil microbiome studies. I also want to highlight a fun research paper (and paired Wired article) on the microbiome of da Vinci’s drawings.

Happy reading! And for all of those in the U.S. who are celebrating the Thanksgiving holiday, please be safe and follow all local COVID precautions.


Multi-site human microbiome

Mycobiome changes in the vitreous of post fever retinitis patients – Arunasri et al. – PLOS ONE

Review: Metabolomics analysis of microbiota-gut-brain axis in neurodegenerative and psychiatric diseases – Konjevod et al. – Journal of Pharmaceutical and Biomedical Analysis

Animal experiments

Cerumen microbial community shifts between healthy and otitis affected dogs – Borriello et al. – PLOS ONE

Plant, root, and soil microbiome

The difference between cellulolytic ‘culturomes’ and microbiomes inhabiting two contrasting soil types – Evdokimova et al. – PLOS ONE

Diversity of bacteria populations associated with different thallus regions of the brown alga Laminaria digitata – Ihua et al. – PLOS ONE

High nitrogen concentration alter microbial community in Allium fistulosum rhizosphere – Zhao et al. – PLOS ONE

Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale – Zhuang et al. – npj Biofilms and Microbiomes

Water and extremophile microbiome

Shifts in methanogenic archaea communities and methane dynamics along a subtropical estuarine land use gradient – Euler et al. – PLOS ONE

Built environment

**The microbiome of Leonardo da Vinci’s drawings: A bio-archive of their history – Piñar et al. – Frontiers in Microbiology

Microbes in the news

**Meet the microbes living on Da Vinci’s iconic sketches – Simon – Wired

Science, publishing, and career

Postdocs under pressure: ‘Can I even do this any more?’ – Woolston – Nature

November 17, 2020

Multi-site human microbiome

Microbiome diversity predicts surgical success in patients with rectovaginal fistula – Leach et al. – International Urogynecology Journal

Human oral microbiome

[REVIEW]Oral Microbiota and Cancer Development – Tuominen & Rautava – Pathobiology

Human vaginal/pregnancy microbiome

Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth – Feehily et al. – npj biofilms and microbiomes

Human gut microbiome

[REVIEW]IBDs and the pediatric age: Their peculiarities and the involvement of the microbiota – Cococcioni et al. – Digestive and Liver Disease

Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers – Byrd et al. – JEM

Species-dependent variation of the gut bacterial communities across Trypanosoma cruzi insect vectors – Arias-Giraldo – PLOS One

Gut Microbiota and Cancer Correlates – Malaviya et al. – Probiotic Research in Therapeutics

Short-Chain Fatty Acids and Lipopolysaccharide as Mediators Between Gut Dysbiosis and Amyloid Pathology in Alzheimer’s Disease – Marizzoni et al. – Journal of Alzheimer’s Disease

Built environment (subways, indoor surfaces)
Unravelling the importance of the eukaryotic and bacterial communities and their relationship with Legionella spp. ecology in cooling towers: a complex network – Paranjape et al. – Microbiome

Techniques
Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities – Kleiner et al. – Microbiome

[REVIEW]NMR: Unique Strengths That Enhance Modern Metabolomics Research – Edison et al. – Analytical Chemistry

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

Study offers “indisputable” link between Alzheimer’s and gut microbiome – Lavars – New Atlas

October 30, 2020

COVID19
Cancer inpatients with COVID-19: A report from the Brazilian National Cancer Institute – de Melo et al. – PLOS One

Few bacterial co-infections but frequent empiric antibiotic use in the early phase of hospitalized patients with COVID-19: results from a multicentre retrospective cohort study in The Netherlands – Karami – et al. – Infectious Diseases

Infection of dogs with SARS-CoV-2 – Sit et al. – Nature

General microbiome/metabolome

Metabolomics of primary cutaneous melanoma and matched adjacent extratumoral microenvironment – Taylor et al. PLOS One

Human gut microbiome

Microbial signature in IgE-mediated food allergies – Goldberg et al. – Genome Medicine

Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy – Rattanathammethee et al. – PLOS One

[Book Chapter]Understanding Polyphenols’ Health Effects Through the Gut Microbiota – Selma et al. – Dietary Polyphenols : Their Metabolism and Health Effects

[REVIEW]Gut Microbiota: Its Potential Roles in Pancreatic Cancer – Li et al. – Front. Cell. Infect. Microbiol.

Plant, root, and soil microbiome

Biological invasions alter environmental microbiomes: A meta-analysis – Malacrino et al. – PLOS One

Phages and viruses

[PREPRINT]VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature – Zablocki et al. – bioRxiv

Mycobiome
[REVIEW]T cell immunity to commensal fungi – Scheffold, Bacher & LeibundGut-Landmann – Current Opinion in Microbiology

Bioinformatics

Prometheus, an omics portal for interkingdom comparative genomic analyses – Ko et al. – PLOS One

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

News in Brie! Scientists discover cheese is so smelly because it helps microbes ‘talk’ to the bacteria that makes it ripe – S. Howes – Daily Mail

October 07, 2020

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 1, 2020

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 25, 2020

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 21st, 2020

God morgon!

Good morning from Sweden. It’s Monday, beginning of a new week and today’s digest carries a lot of preprints with interesting information.

As ususal, new knowledge about COVID-19 keeps pouring in. A library of 1200 small molecules was screened to reveal at least 20 FDA-approved small molecules that can enhance the antiviral activity of remdesivir. A human enzyme was also shown to be involved in antiviral defences. A new preprint also revealed some modifications in the SARS-CoV-2 spike protein that can increase vaccine efficacy.

Continuing with viruses, new preprint report an improved Zika vaccine, a basic study exploring reverse transcription and thereby developing a better system to study anti-HIV drugs, and a new detailed protocol for enriching viromes in water samples.

Also in today’s digest are some preprints on basic bacteriology with reports on (p)ppGpp and persister cells, Streptococcal membranes, secretory products and their role in Listeria virulence, and efflux pumps in Burkholderia.

Apart from these, there are, coincidentally, two reports on microbial diversity of the waters of Shark Bay, Australia, algal diversity in corals, a relationship between termite gut-microbiota and changes in temperature, and the role of gut microbiota in possibly affecting the sexual dimorphism in susceptibility to diseases.

Hope you enjoy the collection!

COVID-19

Preprint: Discovery of SARS-CoV-2 antiviral synergy between remdesivir and approved drugs in human lung cells – Xammy Nguyenla, et al.

Preprint: A trimeric human angiotensin-converting enzyme 2 as an anti-SARS-CoV-2 agent in vitro – Tianshu Xiao, et al.

Preprint: Development of RNA-based assay for rapid detection of SARS-CoV-2 in clinical samples – Vinod Kumar, et al.

Preprint: Introduction of two prolines and removal of the polybasic cleavage site leads to optimal efficacy of a recombinant spike based SARS-CoV-2 vaccine in the mouse model – Fatima Amanat, et al.

Viruses

Preprint: Measles-based Zika vaccine induces long-term immunity and requires NS1 antibodies to protect the female reproductive tract in the mouse model of ZIKA – Drishya Kurup, et al.

Preprint: Cocculus hirsutus-derived phytopharmaceutical drug has potent anti-dengue activity – Ankur Poddar, et al.

Preprint: Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication – Benjamin M. Akiyama, et al.

Preprint: Chemical Stabilization of the HIV-1 Capsid Results in Efficient HIV-1 Reverse Transcription in vitro – Jordan Jennings, et al.

Preprint: Life cycle process dependencies of positive-sense RNA viruses suggest strategies for inhibiting productive cellular infection – Harsh Chhajer, et al.

Preprint: Zika virus NS3 protease and its cellular substrates – Agnieszka Dabrowska, et al.

Preprint: A step-by-step sequence-based analysis of virome enrichment protocol for freshwater and sediment samples – Federica Pinto, et al.

Preprint: Matrix metalloproteinases and tissue inhibitors of metalloproteinases in murine coronavirus-induced neuroinflammation – Sourodip Sengupta, et al.

Bacteria Hysteria

Preprint: The generation of persister cells is regulated at the initiation of translation by (p)ppGpp – Roberto C. Molina-Quiroz and Andrew Camilli.

Preprint: Spontaneous Escherichia coli persisters with week-long survival dynamics and lasting memory of a short starvation pulse – Mikkel Skjoldan Svenningsen, et al.

Preprint: Slipped strand mispairing in the gene encoding cell wall associated sialidase NanH3 in Gardnerella spp – Shakya P. Kurukulasuriya, et al.

Preprint: Membrane linkage of a Streptococcus pneumoniae Wzy capsular polysaccharide occurs through an acylglycerol – Thomas R. Larson and Janet Yother.

Preprint: Fluorescent secreted bacterial effectors reveal active intravacuolar proliferation of Listeria monocytogenes in epithelial cells – Caroline Peron-Cane, et al.

Preprint: Burkholderia collagen-like protein 8, Bucl8, is a unique outer membrane component of a tetrapartite efflux pump in Burkholderia pseudomallei and Burkholderia mallei – Megan E Grund, et al.

Preprint: Cerebrospinal fluid proteome maps detect pathogen-specific host response patterns in meningitis – Anahita Bakochi, et al.

Preprint: Piperacillin/tazobactam resistant, cephalosporin susceptible Escherichia coli bloodstream infections driven by multiple resistance mechanisms across diverse sequence types – Thomas Edwards, et al.

Preprint: Analysis of beta-lactam heteroresistance in CRE suggests a stage in the spectrum of antibiotic resistance – Victor I Band and David S Weiss

Preprint: Mechanism of selectivity reveals novel antifolate drug interactions – Shannon Lynn Kordus, et al.

Preprint: Identification of trans-AT polyketide clusters in two marine bacteria reveals cryptic similarities between distinct symbiosis factors – Dina Kačar, et al.

Preprint: Heterologous production of 1-tuberculosinyladenosine in Mycobacterium kansasii models pathoevolution towards the transcellular lifestyle of Mycobacterium tuberculosis – Marwan Ghanem, et al.

General Microbiome

Preprint: Genomic insights into adaptations of TMA-utilizing methanogens to diverse habitats including the human gut – Jacobo de la Cuesta-Zuluaga, et al.

Preprint: Metagenomic insights into ecosystem function in the microbial mats of Blue Holes, Shark Bay – Gareth S Kindler, et al.

Preprint: Long-term cellulose enrichment selects for highly cellulolytic consortia and competition for public goods – Gina R Lewin, et al.

Preprint: Functional diversity of microboring Ostreobium algae isolated from corals – Anaïs Massé, et al.

Preprint: Experimental warming reduces gut prokaryotic diversity, survival and thermal tolerance of the eastern subterranean termite, Reticulitermes flavipes (Kollar) – Rachel A Arango, et al.

Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status – Jordi Mayneris-Perxachs, et al., Microbiome

Techniques/Models

Preprint: Cre/LoxP-HBV plasmids generating recombinant covalently closed circular DNA genome upon transfection – Robert L. Kruse, et al.

Preprint: A Novel DNA Chromatography Method to Distinguish M. abscessus Subspecies and Macrolide Susceptibility – Mitsunori Yoshida, et al.

Others

Preprint: Phytophthora sojae effector Avr1d functions as E2 competitor and inhibits ubiquitination activity of GmPUB13 to facilitate infection – Yachun Lin, et al.

Preprint: A Volatile Signal Controls Virulence in the Plant Pathogen Pseudomonas syringae pv. syringae and a Strategy for Infection Control in Organic Farming – Simon Sieber, et al.

Preprint: Schistosoma mansoni lysine specific demethylase 1 (SmLSD1) is a druggable target involved in parasite survival, oviposition and stem cell proliferation – G. Padalino, et al.

Preprint: Alterations to the cardiac metabolome induced by chronic T. cruzi infection relate to the degree of cardiac pathology – Kristyn Hoffman, et al.

Preprint: Remarkable recent changes in genetic diversity of the avirulence gene AvrStb6 in global populations of the wheat pathogen Zymoseptoria tritici – Christopher Stephens, et al.

Microbes in News

Soon-to-be-launched microbiome concept symbiome raises $15mm – Beauty Matters

Finch closes $90 million series d to advance C. difficile infection product – Pharma Live

September 9, 2020

SARS-CoV-2

[PREPRINT] Long-term survival of salmon-attached SARS-CoV-2 at 4°C as a potential source of transmission in seafood markets – Dai et al. – bioarxiv

Human gut microbiome

[REVIEW] Predictive values of colon microbiota in the treatment response to colorectal cancer – Galan-Ros et al. – Pharmacogenomics

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

Long-term effects of western diet consumption in male and female mice – Hasegawa et al. – Scientific Reports

Young versus aged microbiota transplants to germ-free mice: increased short-chain fatty acids and improved cognitive performance – Lee et al. – Gut Microbes

Temporal changes in the fecal bacterial community in Holstein dairy calves from birth through the transition to a solid diet – Hennessy et al. – Plos One

Plant, root, and soil microbiome

Comparison of the microbial diversity during two different wine fermentation processes – Böhmer et al. – FEMS Microbiology Letters

[PREPRINT] Functional metagenomics of bark microbial communities from avocado trees (Persea americana Mill.) reveals potential for bacterial primary productivity – Aguirre-von-Wobeser – bioarxiv

Bioinformatics

[PREPRINT] BacAnt: the combination annotation server of antibiotic resistance gene, insertion sequences, integron, transposable elements for bacterial DNA sequences – Hua et al. – bioarxiv

Microbes in the news

Plant-based diets shine when looking at the gut microbiome – Zimlich