September 28, 2020

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


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


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


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


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


*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 initiativeProjects & Presentations

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.


[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


[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

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

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

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!


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.


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


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.


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 17, 2020

Another broad selection of microbiome papers for you this morning. Several papers today show how microbial communities are influenced by pollution, water depth, and El Niño, plus a study that found ants use signals from soil microbes to decide where to nest.

Human gut microbiome

Lactobacillus strains vary in their ability to interact with human endometrial stromal cells, Shiroda and Manning, PLOS ONE

A predictive index for health status using species-level gut microbiome profiling, Vinod K. Gupta et al., Nature Communications

Gut Microbiota and Metabolome Alterations Associated with Parkinson’s Disease, Sarah Vascellari et al., mSystems

Human nearly sterile sites

Metagenome analysis using serum extracellular vesicles identified distinct microbiota in asthmatics, Lee and Choi et al., Scientific Reports

Animal microbiome

The nesting preference of an invasive ant is associated with the cues produced by actinobacteria in soil, Hongmei Huang et al., PLOS Pathogens

Influence of host genetics in shaping the rumen bacterial community in beef cattle, Abbas and Howard et al., Scientific Reports

Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore System, Charlotte B. Francoeur et al., mBio

Plant, root, and soil microbiome

Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts, Shawn M. Higdon et al., PLOS ONE

Water and extremophile microbiome

Pollution shapes the microbial communities in river water and sediments from the Olifants River catchment, South Africa, Angel Valverde et al., Archives of Microbiology

Persistent El Niño driven shifts in marine cyanobacteria populations, Alyse A. Larkin et al., PLOS ONE

Depth-Dependent Variables Shape Community Structure and Functionality in the Prince Edward Islands, Phoma and Makhalanyane, Environmental Microbiology


Preprint: Tracking strains predicts personal microbiomes and reveals recent adaptive evolution, Shijie Zhao et al., bioRxiv

September 13, 2020

Hello from the Sonoran Desert! In today’s digest, you’ll find quite a few exciting reads! In particular, Stepanauskas and collaborators looked at horizontal gene transfer in marine bacterial genomes in a fascinating preprint. They show that marine microorganisms form “gene exchange networks” within which organisms are able to exchange both flexible and core genes, including genes from the rRNA operon! The authors suggest a new definition of microbial species, broader than the current accepted delineation.

Today’s digest also includes few new papers and proceedings presenting novel bioinformatic tools and methods. Among them, Podlevsky and collaborators presents CasCollect, a novel computational tool allowing the assembly and annotation of Cas genes and CRISPR arrays from metagenomic datasets.

Finally, today’s non-biology piece is a very interesting review on the challenge of Big Data in biology: how modern computational frameworks can enable the storage, transfer, access, and analysis of both unstructured and structured massive biological datasets?

Have a great Sunday!

Human vaginal microbiome

Altered vaginal microbiome and relative co-abundance network in pregnant women with penicillin allergy – Li et al. – Allergy , Asthma & Clinical Immunology

Human gut microbiome

Review: Mechanisms underpinning the efficacy of faecal microbiota transplantation in treating gastrointestinal disease – Segal et al. – Therapeutic Advances in Gastroenterology

Animal microbiome

Preprint: Deep-sea mussels from a hybrid zone on the Mid-Atlantic Ridge host genetically indistinguishable symbionts – Uecker et al. – BioRxiV

Metagenomic analysis of viral communities in Baikal sponges – Butina and Bukin – Limnology and Freshwater Biology

Microbial community associated with Baicalian crustacea near gas-oil deepwater discharges – Khalzov et al. – Limnology and freshwater biology

Plant, root, and soil microbiome

Preprint: Investigating the role of root exudates in recruiting Streptomyces bacteria to the Arabidopsis thaliana root microbiome – Worsley et al. – BioRxiV

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

Preprint: Gene exchange networks define species-like units in marine prokaryotes – Stepanauskas et al. – BioRxiV

Preprint: The effects of seasonal anoxia on the microbial community structure in demosponges in a marine lake (Lough Hyne, Ireland) – Schuster et al. – BioRxiV

Food microbiology

Preprint: Diversity and dynamics of fungi during spontaneous fermentations and association with unique aroma profiles in wine – Liu et al. – BioRxiV

Phages and viruses

Depicting the RNA Virome of Hematophagous Arthropods from Belgrade, Serbia – Stanojevic et al. – Viruses

Preprint: An Unconventional Flavivirus and other RNA Viruses in the Sea Cucumber (Holothuroidea; Echinodermata) Virome – Hewson et al. – preprints


Review: Challenges in gene-oriented approaches for pangenome content discovery – Bonnici et al. – Briefings in Bioinformatics

Conference proceedings: A Data Driven Binning Method to Recover More Nucleotide Sequences of Species in a Metagenome – Vimukti et al. – IEEE

CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data – Podlevsky et al – NAR Genomics and bioinformatics


book: Metagenomics: Techniques, Applications, Challenges and Opportunities – Singh et al – Springer Nature Singapore Pte Ltd.

My non-microbiology pick

Review: Big data in biology: The hope and present-day challenges in it Pal et al. – Gene reports

September 11, 2020

Greetings, friends!

This summer I’ve spent a lot of time outside, going on hikes and enjoying nature. Pennsylvania has a high rate of lyme disease so I’m always careful to check myself for ticks after I spend time outdoors. With that in mind, I want to highlight the review article included in today’s digest that focuses on the interactions between Borrelia burgdorgei and ticks. If you’re looking for a book recommendation, Bitten: The Secret History of Lyme Disease and Biological Weapons by Kris Newby is an excellent pairing!

The summer is also a time where many undergraduates gain important research experience. For those of you thinking ahead to next year, today’s digest also includes an article which provides 10 simple rules for an inclusive summer coding program for non-computer-science undergrads.

Finally, I am very excited to promote Black in Microbiology week, which will be held on Twitter and Instagram during the week of September 28th. I’m looking forward to “meeting” lots of new microbiologists and learning about their research! Each day has unique programming and hashtags, so check out the website for more information.

Happy reading!


Black in Micro Week is 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.


Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight – Khan et al. – PLOS One

In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age – Lieberman et al. – PLOS Biology

Factors contributing to healthcare professional burnout during the COVID-19 pandemic: A rapid turnaround global survey – Morgantini et al. – PLOS ONE

General microbiome

Review: Ecology and genomics of Actinobacteria: new concepts for natural product discovery – Bergeijk et al. – Nature Reviews Microbiology

Review: Biofilm dispersion – Rumbaugh & Sauer – Nature Reviews Microbiology

Human respiratory microbiome

Whole-genome sequence of multi-drug resistant Pseudomonas aeruginosa strains UY1PSABAL and UY1PSABAL2 isolated from human broncho-alveolar lavage, Yaoundé, Cameroon – Madaha et al. – PLOS ONE

Human gut microbiome

Regional variations in Helicobacter pylori infection, gastric atrophy and gastric cancer risk: The ENIGMA study in Chile – Herrero et al. – PLOS ONE

A comparative study of the gut microbiome in Egyptian patients with Type I and Type II diabetes – Radwan et al. – PLOS ONE

Animal experiments

Review: Interactions between Borrelia burgdorferi and ticks – Kurokawa et al. – Nature Reviews Microbiology

Antimicrobial resistance in ovine bacteria: A sheep in wolf’s clothing? – Silva et al. – PLOS ONE

Water and extremophile microbiome

Characterization of Vibrio cholerae isolates from freshwater sources in northwest Ohio – Daboul et al. – PLOS ONE

Food microbiology

Characterization of β-lactam resistance in K. pneumoniae associated with ready-to-eat processed meat in Egypt – Abdel-Rhman – PLOS ONE


Ten simple rules for an inclusive summer coding program for non-computer-science undergraduates – Pennings et al. – PLOS Computational Biology

September 10, 2020

Good morning from smokey, apocalyptic San Francisco! The world outside my window may be in sepia tones, but the articles I’m highlighting here are helping to brighten my day. Today’s digest has some fascinating insect and environmental microbiome research including a paper about the gut microbiota of a beetle that lives in the mixed forest of northeastern Asia and its capacity to efficiently degrade polystyrene. Additionally, there’s a paper characterizing the community structure and metabolic capacity of a biofilm-like microbial community lining the wall of the Yumugi river cave in a remote part of Western New Guinea. I’ve also included a paper examining availability of microbial community sequencing data which found that much of this data is not available and offers suggestions for improving data archiving practices. Finally, there is a very interesting technique paper about an orally ingestible microdevice that can be used to sample the gut microbiota in the upper gastrointestinal tract. Happy reading!

General Microbiome
Influence of Intratumor Microbiome on Clinical Outcome and Immune Processes in Prostate Cancer. – Ma, J. et al., Cancers

Experimental (co)evolution in a multi-species microbial community results in local maladaptation. – Castledine, M. et al., Ecology Letters

Pregnancy and Early Life
Mothers of Preterm Infants Have Individualized Breast Milk Microbiota that Changes Temporally Based on Maternal Characteristics. – Asbury, M.R et al., Cell Host Microbe

The meconium microbiota shares more features with the amniotic fluid microbiota than the maternal fecal and vaginal microbiota. – He, Q. et al., Gut Microbes

Skin microbiome
Stratum Corneum Lipidomics Analysis Reveals Altered Ceramide Profile in Atopic Dermatitis Patients Across Body Sites With Correlated Changes in Skin Microbiome. – Emmert, H. et al., Experimental Dermatology

Vaginal microbiome
Diverse vaginal microbiome was associated with pro-inflammatory vaginal milieu among pregnant women in Uganda. – Bayigga, L. et al. Human Microbiome Journal

Gut microbiome
Diet Diurnally Regulates Small Intestinal Microbiome-Epithelial-Immune Homeostasis and Enteritis. – Tuganbeav, T. et al., Cell

Microbiota-modulated CART + enteric neurons autonomously regulate blood glucose. – Muller, P.A. et al., Science

Succinate Produced by Intestinal Microbes Promotes Specification of Tuft Cells to Suppress Ileal Inflammation. -Banerjee, A. et al., Gastroenterology

Animal Experiments
Gut microbiome improves postoperative cognitive function by decreasing permeability of the blood-brain barrier in aged mice. – Wen, J. et al., Brain Research Bulletin

Indolepropionic Acid, a Metabolite of the Microbiome, Has Cytostatic Properties in Breast Cancer by Activating AHR and PXR Receptors and Inducing Oxidative Stress. – Sári, Z. et al., Cancers

Angiogenin maintains gut microbe homeostasis by balancing α-Proteobacteria and Lachnospiraceae. – Sun, D. et al., Gut

Gut Microbiota-Associated Activation of TLR5 Induces Apolipoprotein A1 Production in the Liver. – Yiu, J.H.C. et al., Circulation Research

Animal and insect microbiome
Cross-generational effects of climate change on the microbiome of a photosynthetic sponge. – Luter, H.M. et al., Environmental Microbiology

Symbionts shape host innate immunity in honeybees. – Horak, R.D. et al., Proceedings Biological Sciences

Parental Microbiota Modulates Offspring Development, Body Mass and Fecundity in a Polyphagous Fruit Fly. – Nguyen, B. et al. Microorganisms

Fast and Facile Biodegradation of Polystyrene by the Gut Microbial Flora of Plesiophthalmus davidis Larvae. – Woo, S. et al., Applied and Environmental Microbiology

Gut microbiota protects honey bees (Apis mellifera L.) against polystyrene microplastics exposure risks. – Wang, K. et al., Journal of Hazardous Materials

Plant, root, and soil microbiome
Characteristics of microbial community of soil subjected to industrial production of antibiotics. – Borčinová, M. et al., Folia Microbiologica

Host selection shapes crop microbiome assembly and network complexity. -Xiong, C. et al., The New Phytologist

Microbiome of root vegetables-a source of gluten-degrading bacteria. – Kõiv, V. et al., Applied Microbiology and Biotechnology

Water and extremophile microbiome
Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity. – Wang, Z. et al., ISME Journal

Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth. – Xue, C-X et al., Microorganisms

The microbial community of a biofilm lining the wall of a pristine cave in Western New Guinea. – Turrini, P. et al., Microbiological Research

Built environment
Airborne bacteria in outdoor air and air of mechanically ventilated buildings at city-scale in Hong Kong across seasons. – Zhou, Y. et al., Environmental Science and Technology

Phages and viruses
Review: Phages and their potential to modulate the microbiome and immunity. Federici, S. et al., Cellular and Molecular Immunology

Generalized estimating equation modeling on correlated microbiome sequencing data with longitudinal measures. – Chen, B. and Xu, W., PLoS Computational Biology

The Nubeam reference-free approach to analyze metagenomic sequencing reads. – Dai, H. and Guan, Y., Genome Research

The archives are half-empty: an assessment of the availability of microbial community sequencing data. – Jurburg, S.D. et al., Communications Biology

An effective culturomics approach to study the gut microbiota of mammals. – Pereira, A.C. and Cunha, M.V., Research in Microbiology

Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment. – Reichart, N.J. et al., ISME Journal

An Ingestible Self-Polymerizing System for Targeted Sampling of Gut Microbiota and Biomarkers. – Chen, L. et al., ACS Nano

September 9, 2020


[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


[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

September 4, 2020

Good morning and get ready to enjoy a small, but diverse microbiome digest. Enjoy!

Commentary: Misconceptions about weather and seasonality must not misguide COVID-19 response – Colin J Carlson et al. – Nature Communications

Multi-site human microbiome
Relationship between the composition of the intestinal microbiota and the tracheal and intestinal colonization by opportunistic pathogens in intensive care patients – Candice Fontaine et al. – PLOS One

Human gut microbiome
Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C – Alyssa G. Kent et al. – Nature Communications

Animal experiments
Review: Modulation of gut microbiota in healthy rats after exposure to nutritional supplements – Mirna Cool et al. – Gut Microbes

Animal microbiome
Anthrax toxin component, Protective Antigen, protects insects from bacterial infection – Saleem Alarme – PLOS Pathogens

Environmental gut bacteria in European honey bees (Apis mellifera) from Australia and their relationship to the chalkbrood disease – Sheba Khan et al. – PLOS One

Gut Microbiome Composition is Associated with Age and Memory Performance in Pet Dogs – Eniko Kubinyi et al. – Animals

Plant, root, and soil microbiome
Characterizing the nectar microbiome of the non-native tropical milkweed, Asclepias curassavica, in an urban environment – Magdalena L. Warren et al. – PLOS One

Water and extremophile microbiome
Book chapter:
Analyzing the Diversity of Microbial Communities Residing in Marine Ecosystems – Piyush Chandna et al. – In: Marine Biotechnology

Ten simple rules to power drug discovery with data science – Enrico Ferrero et al. – PLOS Computational Biology

Review: Sample pre-treatment procedures for the omics analysis of human gut microbiota: turning points, tips and tricks for gene sequencing and metabolomics – Elisa Zubeldia-Varela et al. – Journal of Pharmaceutical and Biomedical Analysis

Research Topic: Beyond Conventional Models: Expanding Experimental Systems for Animal-Microbiome Interaction Research