June 2, 2020

Happy Month of June to all,
June serves as the national month for Alzheimer’s and brain awareness. So I will start today’s digest with some news articles about the same.
Further the digest covers some very fascinating research articles about how the microbiome influences transcriptional profile in Drosophila melanogaster to peripheral blood microbial signatures in COPD. Digest also features some awesome microbe related science communication articles.
Enjoy reading!!!
Have a Safe, Healthy, Happy, and Productive month ahead.

Alzheimer’s and brain awareness news posts

Alzheimer’s & Brain Awareness Month 2020 – Bankston – ASBMB Today

Could the gut microbiome be linked to autism? – Svoboda – Nature Outlook

General microbiome
*Interactions between the microbiome and mating influence the female’s transcriptional profile in Drosophila melanogaster – Delbare et al – bioRxiv

Phenotypic changes of bacteria through opportunity and global methylation leads to antibiotic resistance – Neerathilingam et al – bioRxiv

Human nearly-sterile sites
Peripheral blood microbial signatures in COPD – Morrow et al – bioRxiv

Human gut microbiome
Prebiotics and community composition influence gas production of the human gut microbiota – Yu et al – bioRxiv

Short-term High Intensity Interval Training (HIIT) Exercise Does Not Affect Gut Bacterial Community Diversity or Composition of Lean and Overweight Men -Rettedal et al – Experimental Physiology

Animal experiments
Integrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes – Clusinska et al – Communications Biology

Water and extremophile microbiome
Phylum-level Diversity of the Microbiome of the Extremophilic Basidiomycete Fungus Pisolithus Arhizus (Scop.) Rauschert: An Island of Biodiversity in a Thermal Soil Desert – Culling et al – MicrobiologyOpen

Food microbiology
Lactobacillus Rhamnosus 2016SWU.05.0601 Regulates Immune Balance in Ovalbumin-Sensitized Mice by Modulating the Immune-Related Transcription Factors Expression and Gut Microbiota – Song et al – Journal of the Science of Food and Agriculture

Harnessing Ultrasound-Stimulated Phase Change Contrast Agents to Improve Antibiotic Efficacy Against Methicillin-Resistant Staphylococcus aureus Biofilms – Durham et al – bioRxiv

Microbiome Science communication articles
The hunt for a healthy microbiome – Eisenstein – Nature Outlook

The complex relationship between drugs and the microbiome – Savage -Nature Outlook

The Infant Gut Microbiome and Probiotics that Work – Smilowitz and Taft – The Scientist

June 1, 2020

God morgon!

Good morning from Sweden. It’s a new week and a new month! I hope everyone is doing good and staying healthy during these tough times. Like the tradition, today’s digest opens with COVID 19 related articles. There is an interesting Q&A article that provides a lot of important information. There is an article that focused on the disease progression and recovery from COVID in children and found out that Computerized Tomography (CT) may not be the best tool when it comes to analyzing COVID in children. Apart form COVID 19, there is also some new interesting information from the structure of Type-IV pilus. Elsewhere in the digest is an article on an easy to use toolkit for microbiome analysis and development of a new path-breaking point-of-care system for rapid detection of mycobacteria.

Hope you’ll enjoy and learn something new from today’s digest!


Q&A: The novel coronavirus outbreak causing COVID-19 – Dale Fisher and David Heymann – BMC Medicine

Preprint: Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes – Ching-Lin Hsieh, et al.

A single-center, retrospective study of COVID-19 features in children: a descriptive investigation – Huijing Ma, et al. – BMC Medicine

Quantifying the impact of physical distance measures on the transmission of COVID-19 in the UK – Christopher I. Jarvis, et al. – BMC Medicine

General Microbiome

Preprint: Microbial strategies for survival in the glass sponge Vazella pourtalesii – Kristina Bayer, et al.

Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria – Xingxing Jian, et al. – Microbiome


Preprint: Oropouche virus glycoprotein topology and cellular requirements for virus-like particle assembly – Natalia da silva barbosa, et al.


Preprint: Competition and Caries on Enamel of a Dual-species Biofilm Model of Streptococcus mutans and Streptococcus sanguinis – Natalia Díaz-Garrido, et al.

Preprint: Investigations of dimethylglycine (DMG), glycine betaine and ectoine uptake by a BCCT family transporter with broad substrate specificity in Vibrio species – Gwen Gregory, et al.

Preprint: TsaP binds PilQ and is involved in cyclic di-GMP signaling – Matthew McCallum, et al.

Preprint: SoxS represses flagellar gene expression through RflP in Salmonella enterica Serovar Typhimurium – Srinivas S Thota, et al.

Preprint: Towards Mycobacterium tuberculosis detection at the point-of-care: a brighter solvatochromic probe permits the detection of mycobacteria within minutes – Mireille Kamariza, et al.


Preprint: animalcules: Interactive Microbiome Analytics 1 and Visualization in R – W. Evan Johnson, et al.

May 31, 2020

Human microbiome

The interplay between immune system and microbiota in gynecological diseases: a narrative review – Villa et al. – European Review for Medical and Pharmacological Sciences

Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians –  Rubel et al. – Genome Biology

Ethnic diversity in infant gut microbiota is apparent before the introduction of complementary diets – Xu et al. – Gut Microbes

Dissimilarity of Airway and Lung Tissue Microbiota in Smokers undergoing Surgery for Lung Cancer – Reinhold et al. – Microorganisms

Chemotherapy-induced ileal crypt apoptosis and the ileal microbiome shape immunosurveillance and prognosis of proximal colon cancer – Roberti et al. – Nature Medicine

Animal microbiome

Characterization of the bacterial microbiota composition and evolution at different intestinal tract in wild pigs (Sus scrofa ussuricus) – Yang et al. – PeerJ

Dietary Soluble and Insoluble Fiber With or Without Enzymes Altered the Intestinal Microbiota in Weaned Pigs Challenged With Enterotoxigenic E. coli F18 – Li et al. – Frontiers in Microbiology

The Dynamics of Interacting Bacterial and Fungal Communities of the Mouse Colon Following Antibiotics – Nettles et al. – Microbial Ecology

Food microbiome

Assessment of overall microbial community shift during Cheddar cheese production from raw milk to aging – Choi et al. – Applied Microbiology and Biotechnology

Marine microbiome

Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan – Sichert et al. – Nature Microbiology

Scientific communication and education

Preprint: A rapid urban biodiversity blitz using aquatic environmental DNA – Hupalo et al. – bioRxiv

Preprint: The representation of women as authors of submissions to ecology journals during the COVID-19 pandemic – Fox – bioRxiv

May 30, 2020

Greetings from Colorado. Today the Microbiome Digest brings you a variety of the latest microbiome-related publications including the human tumor microbiome by Nejman et al., microbial colonization in the neonatal gut microbiome by Wang and Dominguez-Bello, and drought effects on the millet root microbiome together with many more interesting papers. Enjoy.


Antimicrobial resistance in the age of COVID-19 – Editorial – Nature Microbiology

Metatranscriptomic Characterization of COVID-19 Identified A Host Transcriptional Classifier Associated With Immune Signaling – Zhang et al. – Clinical Infetious Diseases

General microbiome

Monitoring the microbiome for food safety and quality using deep shotgun sequencing – Beck et al. – bioRxiv

Fecal microbiota transplantation efficacy for Clostridium difficile infection: A trans-kingdom battle between donor and recipient gut microbiomes– Kazemian et al. – bioRxiv

Human microbiome

The human tumor microbiome is composed of tumor type–specific intracellular bacteria – Nejman et al. – Science*

Animal experiments

Pathogenesis, transmission and response to re-exposure of SARS-CoV-2 in domestic cats – Bosco-Lauth et al. – bioRxiv

The heart microbiome of insectivorous bats from Central and South Eastern Europe – Corduneanu et al. – bioRxiv

Gut microbiome

Microbial colonization alters neonatal gut metabolome – Wang and Dominguez-Bello – Nature Microbiology

Plant, root, and soil microbiome

Breeding for resistance: can we increase crop resistance to pathogens without compromising the ability to accommodate beneficial microbes? – Zuccaro and Langen – New Phytologist

Experimental assessment of tree canopy and leaf litter controls on the microbiome and nitrogen fixation rates of two boreal mosses – Jean et al. – New Phytologist

Drought Drives Spatial Variation in the Millet Root Microbiome – Simmons et al. – Frontiers in Plan Science*

Streptomyces’ scent attracts spore dispersers – Rohlfs – Nature Microbiology*

Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts – Higdon et al. – bioRxiv

May 29, 2020

Good Friday, everyone. Today the Microbiome Digest brings you a variety of the latest microbiome-related publications. Have a nice weekend.


Treatments in the COVID-19 pandemic: an update on clinical trials – Tao – Expert Opinion on Emerging Drug

Ozone Treatment for Elimination of Bacteria and SARS-CoV2 for Medical Environments – Westover et al. – bioRxiv

Coronavirus, as a source of pandemic pathogens – Konishi – bioRxiv

Nature news

Are women publishing less during the pandemic? Here’s what the data say

Coronavirus vaccine trials have delivered their first results — but their promise is still unclear

How to address the coronavirus’s outsized toll on people of colour

Human Microbiome

The role of gastric microbiota in gastric cancer – Stewart et al. – Gut Microbes

Ongoing Supplementation of Probiotics to Cesarean-Born Neonates during the First Month of Life may Impact the Gut Microbial – Yan et al. – Am J Perinatol

Animal experiments

Genetics but not intestinal microbiota determines the onset of systemic autoimmune disease in BXD2 mice – Hong et al. – The Journal of Immunology

Metabolic cooperation among commensal bacteria supports Drosophila juvenile growth under nutritional stress – Consuegra et al. – bioRxiv

Animal microbiome

Exploring the eukaryotic diversity in rumen of Indian camel (Camelus dromedarius) using 18S rRNA amplicon sequencing – Mishra et al. – Archives of Microbiology

Microbial metabolomics

IBD Microbial Metabolome: The Good, Bad, and Unknown – Sidebottom and Chang – Trends in Endocrinology & Metabolism

Environmental microbiology

Microbial Consortiums of Hydrogenotrophic Methanogenic Mixed Cultures in Lab-Scale Ex-Situ Biogas Upgrading Systems under Dierent Conditions of Temperature, pH and CO – Xu et al. – Microorganisms

Plant, root, and soil microbiome

Livestock grazing abandonment reduces soil microbial activity and carbon storage in a Mediterranean Dehesa – Oggioni et al. – Applie Soil Ecology

Halotolerant plant growth–promoting bacteria: Prospects for alleviating salinity stress in plants – Etesami & Glick – Environmental and Experimental Botany

Fertilization changes soil microbiome functioning, especially phagotrophic protists – Zhao et a. – Soil Biology and Biochemestry

Effect of combined application of organic and inorganic phosphatic fertilizers on dynamic of microbial biomass in semi-arid soil – Khosa et al.- Soil Science Annual

High levels of primary biogenic organic aerosols are driven by only a few plant-associated microbial taxa – Abdoulaye et al. – Atmospheric Chemestry & Physics

Complexity of bacterial and fungal network increases with soil aggregate size in an agricultural Inceptisol – Liao et al. – Applied Soil Ecology

Azole use in agriculture reduces Aspergillus fumigatus abundance but does not alter its population structure – Barber et al. – bioRxiv


Food microbiology

Novel Approaches to Minimising Mycotoxin Contamination – Jovita and Nunez – Toxins

Mentholation triggers brand-specific shifts in the bacterial microbiota of commercial cigarette products – Malayil et al. – Applied Microbial and Cell Physiology

May 23, 2020

Good Saturday, everyone. Today the Microbiome Digest brings you the latest on plant-microbial interaction and environmental microbiology together with a variety of your usual microbiome related publications. Enjoy!.

Human respiratory microbiome

A prevalent and culturable microbiota links ecological balance to clinical stability of the human lung after transplantation -Das et al.- bioRxiv

Human gut microbiome

A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities -Barlow et al.- Nature Communications

Gut Microbiota and Disorders of the Central Nervous System – Vuotto et al.- Neuroscientist

Animal experiments

Intestinal fungi are causally implicated in microbiome assembly and immune development in mice– Erik van Tilburg Bernardes et al.- Nature Communications

Linking perturbations to temporal changes in diversity, stability, and compositions of neonatal calf gut microbiota: prediction of diarrhea -Ma et a.- ISME

Built environment

Continental-scale microbiome study reveals different environmental characteristics determining microbial richness and composition/quantity in hotel rooms -Fu et al.- mSystems

Environmental Microbiology

Extreme storms cause rapid, context-dependent shifts in nearshore subtropical bacterial communities -Ares et al.- bioRxiv

Mimicking climate warming effects on Alaskan soil microbial communities via gradual temperature increase – Ballhausen et al.- Scientific Reports

Plant, root, and soil microbiome

Deciphering the root endosphere microbiome of the desert plant Alhagi sparsifolia for drought resistance-promoting bacteria -Zhang et al.- Applied and

Drought and plant litter chemistry alter microbial gene expression and metabolite production -Malik et al.- ISME

Genome-scale metabolic reconstruction of the symbiosis between a leguminous plant and a nitrogen-fixing bacterium– DiCenzo et al.- Nature Communications

May 22, 2020

We’ve got a decently sized digest today with a lot of environmental microbe papers, including descriptions of novel species. There is also the Cell paper (highlighted) from Peter Turnbaugh’s group on ketogenic diets and the gut microbiome, which has been getting a lot of press. For new bioinformatic and other techniques, we have a new R package to predict functional profiles in Tax4Fun2, an assessment of phylogenetic rooting methods for bacteria, and a description of fiber intervention used in undergraduate classes for active learning.

 Have a great weekend!


Today is the last day of the Virtual Microbiome Summit.

Pregnancy and early life

Women’s multisite microbial modulation during pregnancy – Luiz G. Sparvoli – Microbial Pathogenesis

Multi-site human microbiome

Review: Bi-Directional Interactions Between Microbiota and Ionizing Radiation in Head and Neck and Pelvic Radiotherapy-Clinical Relevance – Nidhya Teresa Joseph – International Journal of Radiation Biology

Human oral microbiome

Defining the oral microbiome by whole-genome sequencing and resistome analysis: the complexity of the healthy picture – Elisabetta Caselli – BMC Microbiology

Human gut microbiome

Ketogenic diets alter the gut microbiome resulting in decreased intestinal Th17 cells – Qi Yan Ang – Cell

Preprint: Host genetic and environmental factors shape the human gut resistome – Caroline I. Le Roy – bioRxiv

MinION Sequencing of colorectal cancer tumour microbiomes—A comparison with amplicon-based and RNA-Sequencing – William S. Taylor – PLOS One (Originally posted to the Digest as a pre-print, now published)

Animal experiments

Broilers divergently selected for digestibility differ for their digestive microbial ecosystems – Marion Borey – PLOS One

Dietary Isomalto/Malto‐Polysaccharides Increase Fecal Bulk and Microbial Fermentation in Mice – Rima H. Mistry – Molecular Nutrition and Food Research

Longitudinal Effects of Dietary Oxidized Lipids on the Gut Microbiome and Mycobiome in Pigs – Folagbayi Arowolo – FASEB Journal

Animal microbiome

Single-cell amplicon sequencing reveals community structures and transmission trends of protist-associated bacteria in a termite host – Michael E. Stephens – PLOS One

Plant, root, and soil microbiome

Xylella fastidiosa subsp. pauca and olive produced lipids moderate the switch adhesive versus non-adhesive state and viceversa – Valeria Scala – PLOS One

Mitochondrial genome sequence of Phytophthora sansomeana and comparative analysis of Phytophthora mitochondrial genomes – Guohong Cai – PLOS One

nirS-type denitrifying bacterial communities in relation to soil physicochemical conditions and soil depths of two montane riparian meadows in North China. – Xiaoli Han – Environmental Science and Pollution Research

Tissue-Specific Dynamics in the Endophytic Bacterial Communities in Arctic Pioneer Plant Oxyria digyna – Cindy Given – Frontiers in Plant Science

Effects of Cultured Root and Soil Microbial Communities on the Disease of Nicotiana tabacum Caused by Phytophthora nicotianae – Tianbo Liu – Frontiers in Microbiology

Novel putative rhizobial species with different symbiovars nodulate Lotus creticus and their differential preference to distinctive soil properties – M Rejili – FEMS Microbiology Letters

Water, air, and extremophile microbiome

The microbiome of alpine snow algae shows a specific inter-kingdom connectivity and algae-bacteria interactions with supportive capacities – Lisa Krug – ISME Journal

Variation of near surface atmosphere microbial communities at an urban and a suburban site in Philadelphia, PA, USA – JD Stewart – Science of the Total Environment

Pilot-scale petroleum refinery wastewaters treatment systems: performance and microbial communities’ analysis – Fatma Karray – Process Safety and Environmental Protection

Adverse effects of levofloxacin and oxytetracycline on aquatic microbial communities – Zhigao Zhou – Science of the Total Environment

Application of microbial network analysis to discriminate environmental heterogeneity in Fildes Peninsula, Antarctica – Qian Liu – Marine Pollution Bulletin

Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium – HS Tee – ISME Journal

Metabolic diversity and co-occurrence of multiple Ferrovum species at an acid mine drainage site – Christen L. Grettenberger – BMC Microbiology

Halocatena pleomorpha gen. nov. sp. nov., an extremely halophilic archaeon of family Halobacteriaceae isolated from saltpan soil – Ashish Verma – IJSEM

Unveiling Cultivable and Uncultivable Halophilic Bacteria Inhabiting Marakkanam Saltpan, India and Their Potential for Biotechnological Applications – Jojy John – Geomicrobiology Journal

Flavobacterium profundi sp. nov., isolated from a deep-sea seamount – Qian Wang – IJSEM

Food microbiology

Molecular epidemiology, genetic diversity and antimicrobial resistance of Staphylococcus aureus isolated from chicken and pig carcasses, and carcass handlers – Onyinye J. Okorie-Kanu – PLOS One

Traditional milk transformation schemes in Côte d’Ivoire and their impact on the prevalence of Streptococcus bovis complex bacteria in dairy products – Aimé R Sanhoun – PLOS One

Comparison of Microbial Communities and Amino Acid Metabolites in Different Traditional Fermentation Starters Used during the Fermentation of Hong Qu Glutinous Rice Wine – Zhang-Cheng Liang – Food Research International

Preprint: Monitoring the microbiome for food safety and quality using deep shotgun sequencing – Kristen L. Beck – bioRxiv


Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)? – Ping Liu – PLOS Pathogens

Vector competence of Aedes aegypti from New Caledonia for the four recent circulating dengue virus serotypes – Olivia O’Connor – PLOS Neglected Tropical Diseases


Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences – Franziska Wemheuer – Environmental Microbiome


Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families – Taylor Wade – PLOS One

Science education techniques: Fiber Force: A Fiber Diet Intervention in an Advanced Course-Based Undergraduate Research Experience (CURE) Course – Julia Massimelli Sewall – Journal of Microbiology & Biology Education

Science and art

This photographer creates prints with algae.

Non-microbiology picks:

Herd of fuzzy green “glacier mice” baffles scientists.