March 15th, 2021

God morgon!

Good morning from Sweden. Another Monday, a new week, and a new digest.

Today’s digest comes with a new review on gut microbiota focusing on the mycobiota which is mostly overlooked as a bulk of studies focus their interest on bacterial diversity in the gut instead. A very cool feature, which I think is now fast becoming common in papers published in Microbiome is the use of a very informative video abstract. As I mentioned in my previous digest, a video abstract catches the eye and it could very well be the next big thing in academic publishing.

There is some potential bad news from Brazil as a team has identified a new nCoV variant of interest (VoI) which probably originated in August 2020 and accounted for about 3% of all samples analyzed between November 2020 and February 2021. The variant also accounted for a very high fraction (35%) of all the B.1.1.33 lineage samples analyzed during the aforementioned period and is now considered widely distributed in Brazil. The troubling fact is that this variant has a S:E484K mutation in the spike protein and this mutation has been implicated in immune evasion and resistance to several monoclonal antibodies. Speaking about COVID-19, there is a new study that tested the viability of nCoV on various inanimate surfaces. The virus persisted longest on a surgical mask (for about 124 hours) and reduced the fastest on a polyester shirt (about 2.5 hours).

Elsewhere in the digest is a preprint that analysed publically available datasets to determine the effect of space type radiation on the gut microbiome, a somewhat controversial study (check out the comments section) hypothesizing the use of fungus to attenuate ionizing radiation on the ISS, and a comprehensive study of E. coli phage-host interactions within the BASEL phage collection.

Hope you’ll enjoy today’s digest.

Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities – Xiaoyan Wu, et al., Microbiome

Preprint: A potential SARS-CoV-2 variant of interest (VOI) harboring mutation E484K in the Spike protein was identified within lineage B.1.1.33 circulating in Brazil – Paola C Resende, et al.

Preprint: Persistence of SARS-CoV-2 virus and viral RNA on hydrophobic and hydrophilic surfaces and investigating contamination concentration – Susan Elizabeth Paton, et al.

Preprint: Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection – Enea Maffei, et al.

Preprint: PulseNet international: the missing link between PFGE and WGS – Ibrahim El-khalil M Adam

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

Preprint: A Self-Replicating Radiation-Shield for Human Deep-Space Exploration: Radiotrophic Fungi can Attenuate Ionizing Radiation aboard the International Space Station – Graham K. Shunk, Xavier R. Gomez, and Nils J. H. Averesch

Preprint: Resistance to aztreonam in combination with non-β-lactam β-lactamase inhibitors due to the layering of mechanisms in Escherichia coli identified following mixed culture selection – Ching Hei Phoebe Cheung, et al.

Preprint: Yersinia pestis lipopolysaccharide remodeling confers resistance to a Xenopsylla cheopis cecropin – Basil Mathew, Kari L. Aoyagi, and Mark A. Fisher

Preprint: Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults – Benjamin A Siranosian, et al.

Preprint: Radiation Threats to Humans in Space and an alternative approach with Probiotics – Dilara Diken, et al.

March 5, 2021

Human microbiome

A multi-omic investigation of male lower urinary tract symptoms: Potential role for JC virus – Thomas S. et al. – PLOS ONE

Association between physical activity and changes in intestinal microbiota composition: A systematic review – Aya V. et al. – PLOS ONE

Plant microbiome

Specialized microbiomes facilitate natural rhizosphere microbiome interactions counteracting high salinity stress in plants – Santos S. et al. – Environmental and Experimental Botany


Impact of sampling depth on pathogen detection in pit latrines – Capone D. et al. – PLOS Neglected Tropical Diseases

A novel methodology to study antimicrobial properties of high-touch surfaces used for indoor hygiene applications—A study on Cu metal – Chang T. et al. – PLOS ONE

Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation – Wilson R. M. et al. – PLOS ONE

Animal microbiome

Wastewater treatment works change the intestinal microbiomes of insectivorous bats – Mehl C. et al. – PLOS ONE

Microbial communities developing within bulk sediments under fish carcasses on a tidal flat – Kawamoto Y. et al. – PLOS ONE

Host-microbe interactions

Host-microbe cross-talk governs amino acid chirality to regulate survival and differentiation of B cells – Suzuki M. et al. – Science Advances


An integrated, modular approach to data science education in microbiology – Dill-McFarland, K. A. et al. – PLOS Computational biology


Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes – Salvato, F. et al. – PLOS Pathogens

March 1st, 2021

God morgon!

Good morning from Sweden. It is hard to believe that it has been a year since the unprecedented happenings of March 2020 but regardless of how we see it, time flies!

The most interesting read of the day is a study that conclusively proves that the oral microbiota is not influenced by your genetics, but by environmental factors. I was intrigued by the use of a video byte, a small video abstract of the paper, which is something new for me. In my opinion, it could very well be the next big thing in academic publishing as it took me just two minutes to understand the whole study! Do check it out!

A promising study is in a preprint where the researchers show that the pre-colonization with a less virulent strain of Clostridioides difficile protects model organisms from subsequent lethal colonization of C. difficile. This has important therapeutic implications in case of nosocomial, antibiotic-promoted diarrhea. Another exciting study shows the influence of gut microbiome on colorectal cancer. The researchers showed that the transplant of ‘good’ microbiota from healthy donors could even reduce the tumorigenesis in the disease models.

Elsewhere in the digest are studies on microbiome of tropical marine sediments, novel proteins from human intestinal microbiome, virulence factors of Trypanosoma brucei, and new therapeutic epitopes in N1 neuraminidase of Influenza virus.

Happy reading!

Bacteria Hysteria

Preprint: Protection from lethal Clostridioides difficile infection via intraspecies competition for co-germinant – Jhansi L. Leslie, et al.

Preprint: Fiber-associated Lachnospiraceae reduce colon tumorigenesis by modulation of the tumor-immune microenvironment – Ana S Almeida, et al.

Preprint: G9a and Sirtuin6 epigenetically modulate host cholesterol accumulation to facilitate mycobacterial survival – Praveen Prakhar, et al.

Preprint: Identification of a chromosomally-encoded sucrose operon-like gene cluster in Vibrio parahaemolyticus strain PH05 isolated from Negros Island, Philippines – Czarina Anne E. De Mesa, et al.

Preprint: Gene flux and acid-imposed selection are the main drivers of antimicrobial resistance in broiler chicks infected with Salmonella enterica serovar Heidelberg – Adelumola Oladeine, et al.

Preprint: Analyses of the complete genome sequence of 2,6-dichlorobenzamide (BAM) degrader Aminobacter sp. MSH1 suggests a polyploid chromosome, phylogenetic reassignment, and functions of (un)stable plasmids – Tue Kjærgaard Nielsen, et al.

Preprint: Growth response and recovery of Corynebacterium glutamicum colonies on single-cell level upon defined pH stress pulses – Sarah Täuber, et al.

Preprint: Comparative genomics analysis of Chryseobacterium sp. KMC2 reveals metabolic pathways involved in keratinous utilization and natural product biosynthesis – Dingrong Kang, et al.

Preprint: Calprotectin-mediated zinc chelation inhibits Pseudomonas aeruginosa protease activity in cystic fibrosis sputum – Danielle M. Vermilyea, et al.

General Microbiome

Acquisition of oral microbiota is driven by environment, not host genetics – Chiranjit Mukherjee, et al., Microbiome

Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation – Richa Kaushal, et al., Microbiome

The bacterial communities of Alaskan mosses and their contributions to N2-fixation – Hannah Holland-Moritz, et al., Microbiome

Preprint: A Tad-like apparatus is required for contact-dependent prey killing in predatory social bacteria – Sofiene Seef, et al.

Preprint: Completion of the gut microbial epi-bile acid pathway – Heidi L. Doden, et al.

Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome – Hannes Petruschke, et al., Microbiome

Metagenomics and Bioinformatics

Preprint: Beyond taxonomic identification: integration of ecological responses to a soil bacterial 16S rRNA gene database – Briony A. Jones, et al.

Preprint: Amplicon sequence variants artificially split bacterial genomes into separate clusters – Patrick D. Schloss

Preprint: Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques – Alyssa M Demko, Nastassia V Patin, and Paul R. Jensen.


Preprint: The Epstein-Barr virus ubiquitin deconjugase BPLF1 regulates the activity of Topoisomerase II during virus replication – JInlin Li, et al.

Preprint: Novel epitopes of human monoclonal antibodies targeting the influenza virus N1 neuraminidase – Ericka Kirkpatrick Roubidoux, et al.


Preprint: Organotypic endothelial adhesion molecules are key for Trypanosoma brucei tropism and virulence – Mariana De Niz, et al.

February 24, 2021

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

General microbiome

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

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

Human microbiome

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

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

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

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

Animal microbiome

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

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

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

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

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

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

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

Functional Foods

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

Water microbiome

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


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

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

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

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

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

February 15th, 2021

God morgon!

Good morning from ice-cold Sweden.

Today’s digest carries interesting preprints on microbiology. I really liked reading the report on a bacteriophage cocktail that kills Listeria without affecting the commensal microbiota and a novel rifampin derivative that is active against doxycycline resistant Francisella. Some preprints highlight the basic biology of bacteria. There is a study on genomic evolution in one of the most important bacterial species – Streptomyces, report on endopeptidases in E. coli, and more reports on methods for studying and annotating antibiotic resistance genes.

Elsewhere in the digest are prediction models for drug interaction iin Tuberculosis, interkingdom biofilms by Candida and Lactobacillus, and microbiome studies on human milk, metazoan-microbe interactions, and some marine microbes.

Finally, there is an interview with Pae-Ji soo, the CEO of Genome and Company who talks about the importance of microbiome in modulating the immunotherapy.

Happy reading!

Bacteria hysteria

Preprint: A bacteriophage cocktail significantly reduces Listeria monocytogenes without deleterious impact on the commensal gut microbiota under simulated gastro-intestinal conditions – Rasmus Riemer Jakobsen, et al.

Preprint: TPR1, a novel rifampin derivative demonstrates efficacy alone and in combination with doxycycline against the NIAID Category A Priority Pathogen F. tularensis – Jason E. Cummings, et al.

Preprint: A nadA mutation confers nicotinic acid auxotrophy in pro-carcinogenic intestinal Escherichia coli NC101 – Lacey R Lopez, et al.

Preprint: A non-adaptive demographic mechanism for genome expansion in Streptomyces – Mallory J Choudoir, et al.

Preprint: Role of endopeptidases in peptidoglycan synthesis mediated by alternative cross-linking enzymes in Escherichia coli – Henri Voedts, et al.


Preprint: In vivo generation of BK and JC polyomavirus defective viral genomes in human urine samples associated with higher viral loads – Amin Addetia, et al.

Preprint: Methane-derived carbon flow through host-virus trophic networks in soil – Sungeun Lee, et al.

Preprint: Genome sequencing of the bacteriophage CL31 and interaction with the host strain Corynebacterium glutamicum ATCC 13032 – Max Hünnefeld, et al.

General microbiome

Preprint: Chlorine inactivation of Escherichia coli O157:H7 in fresh produce wash process: effectiveness and modeling – Mohammadreza Dehghan Abnavi, et al.

Subcellular view of host–microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan–microbe symbiosis – Meggie Hudspith, et al., Microbiome

Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes – I. Raimundo, et al., Microbiome

Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota – Shirin Moossavi, et al., Microbiome

Preprint: Do size and shape matter? Exploring the interactions and the metabolome of the soil isolate Hylemonella gracilis – Olaf Tyc, et al.


Preprint: Modelling the impact of the macroalgae Asparagopsis taxiformis on rumen microbial fermentation and methane production – Rafael Muñoz-Tamayo, et al.

Preprint: Transcriptome signature of cell viability predicts drug response and drug interaction for Tuberculosis – Vivek Srinivas, et al.

Preprint: Chemical ecology of a tripartite symbiosis – Nicholas C Mucci, et al.

Preprint: Mapping global shifts in Saccharomyces cerevisiae gene expression across asynchronous time trajectories with diffusion maps – Taylor Reiter, et al.

Preprint: Recurrent Vulvovaginal Candidiasis; a dynamic interkingdom biofilm disease of Candida and Lactobacillus
Emily McKloud, et al.


Preprint: Genie: An interactive real-time simulation for teaching genetic drift – Andreina I Castillo, et al.

Preprint: Direct-from-specimen microbial growth inhibition spectrums under antibiotic exposure and comparison to conventional antimicrobial susceptibility testing – Jade Chen, et al.

HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes – Yu Li,et al., Microbiome


Microbiome to be game changer in immunotherapy‘ : The Korean Times

February 8, 2021

Good morning from Minneapolis!

Today’s microbiome digest includes several interesting research and review articles. Enjoy reading!

General microbiome

Review: The intestinal neuro-immune axis: crosstalk between neurons, immune cells, and microbes – Amanda Jacobson – Mucosal Immunology

Review: The Role of the Gut Microbiome, Immunity, and Neuroinflammation in the Pathophysiology of Eating Disorders – Michael J. Butler – Nutrients

Review: The microbiome and host mucosal interactions in urinary tract diseases – Bernadette Jones-Freeman – Mucosal Immunology

Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota – Francesco Durazzi – Scientific Reports

Perspective: Modulating gut microbiota to treat cancer – Christopher H. Woelk – Science

Sequence Meets Function—Microbiota And Cardiovascular Disease – Myungsuk Kim – Cardiovascular Research

Human gut microbiome

Fecal microbiota transplant overcomes resistance to anti–PD-1 therapy in melanoma patients – Diwakar Davar – Science

Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients – Erez N Baruch – Science

Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt – Simone Rampelli – Communications Biology

Meta-omics characteristics of intestinal microbiota associated to HBeAg seroconversion induced by oral antiviral therapy – Yu-Li Zeng – Scientific Reports

Anti-cancer and anti-inflammatory effects elicited by short chain fatty acids produced by Escherichia coli isolated from healthy human gut microbiota – Atchareeya Nakkarach – Microbial Cell Factories

Exploiting the Microbiota for the Diagnosis of Anal Precancerous Lesions in Men Who Have Sex With Men – Raquel Ron – Journal of Infectious Disease

Distribution characteristics of intestinal microbiota during pregnancy and postpartum in healthy women – Shengtang Qin – The Journal of Maternal-Fetal & Neonatal Medicine

Co-Occurrence of Symptoms and Gut Microbiota Composition Before Neoadjuvant Chemotherapy and Radiation Therapy for Rectal Cancer: A Proof of Concept – Velda J Gonzalez-Mercado – Biological Research For Nursing

Oral and respiratory microbiome

Development of a robust protocol for the characterization of the pulmonary microbiota – Nathan Dumont-Leblond – Communications Biology

Lung microbiota associations with clinical features of COPD in the SPIROMICS cohort – Kristopher Opron – npj Biofilms and Microbiomes

Animal microbiome / Animal experiments

Changes in the gut microbial community of the eastern newt (Notophthalmus viridescens) across its three distinct life stages – Samantha S Fontaine – FEMS Microbiology Ecology

Altered Gut Microbiota is Involved in the Anti‐Hypertensive Effects of Vitamin C in Spontaneously Hypertensive Rat – Ying Li – Molecular Nutrition and Food Research

Long Term High Protein Diet Feeding Alters the Microbiome and Increases Intestinal Permeability, Systemic Inflammation and Kidney Injury in Mice – Matthew Snelson- Molecular Nutrition and Food Research

Low-dose exposure of glyphosate-based herbicides disrupt the urine metabolome and its interaction with gut microbiota – Jianzhong Hu – Scientific Reports

Metagenomics of antimicrobial and heavy metal resistance in the cecal microbiome of fattening pigs raised without antibiotics – Paiboon Tunsagool – Applied and Environmental Microbiology

IL-17 controls central nervous system autoimmunity through the intestinal microbiome – Tommy Regen – Science Immunology

The skin microbiome of Xenopus laevis and the effects of husbandry conditions – Maya Z. Piccinni – Animal Microbiome

Effects of dietary oregano essential oil supplementation on growth performance, intestinal antioxidative capacity, immunity and intestinal microbiota in yellow-feathered chickens – Dong Ruan – Journal of Animal Science

Composition and acquisition of the microbiome in solitary, ground-nesting alkali bees – Karen M. Kapheim – Scientific Reports

The impact of the gut microbiome on memory and sleep in Drosophila – Valeria Silva – Journal of Experimental Biology

Probiotics / prebiotics

Prebiotic dietary fibre intervention improves fecal markers related to inflammation in obese patients: results from the Food4Gut randomized placebo-controlled trial – Audrey M. Neyrinck – European Journal of Nutrition

Plant, root, and soil microbiome

Reduced tillage, cover crops and organic amendments affect soil microbiota and improve soil health in Uruguayan vegetable farming systems – Victoria Cerecetto – FEMS Microbiology Ecology

Tillage shapes the soil and rhizosphere microbiome of barley – but not its susceptibility towards Blumeria graminis f. sp. Hordei – Nina Bziuk – FEMS Microbiology Ecology

The rhizosphere microbiome plays a role in the resistance to soil-borne pathogens and nutrient uptake of strawberry cultivars under field conditions – Cristina Lazcano – Scientific Reports

16S rRNA gene-based microbiome analysis identifies candidate bacterial strains that increase the storage time of potato tubers – Franziska Buchholz – Scientific Reports

Methods and techniques

Boolean implication analysis unveils candidate universal relationships in microbiome data – Daniella Vo – BMC Bioinformatics

Review: Advances in modelling the human microbiome–gut–brain axis in vitro – Chrysanthi-Maria Moysidou

MB-GAN: Microbiome Simulation via Generative Adversarial Network – Ruichen Rong – GigaScience

February 4, 2021

Greetings from a very snowy Pittsburgh!

If you like getting dirty, today’s digest is for you! It includes a review on bat guano, two research articles about compost, four focused on soil research, and a preprint about fertilization with poultry manure.

Happy reading!

Events and jobs

February 1st to 14th: If you’re on twitter, check out #MicrobeValentinesDay! @AnneAMadden is posting 14 days of pink microbes in honor of Valentine’s Day under this hashtag!

Human skin microbiome

Gut microbiome profile in psoriatic patients treated and untreated with biologic therapy – Valentini et al. – The Journal of Dermatology

Human gut microbiome

Preprint – Impact of a human gut microbe on Vibrio cholerae host colonization through biofilm enhancement – Barrasso et al. – bioRxiv

Review: Gut microbiota-mediated pesticide toxicity in humans: methodological issues and challenges in risk assessment of pesticides – Utembe and Kamng’ona – Chemosphere

Animal experiments

Effects of thallium exposure on intestinal microbial community and organ functions in zebrafish (Danio rerio) – Wang et al. – Elementa: Science of the Anthropocene

Is intestinal bacterial diversity enhanced by trans-species spread in the mixed-species flock of hooded crane (Grus monacha) and bean goose (Anser fabalis) wintering in the lower and middle Yangtze river floodplain? – Yang and Zhou – Animals

Animal microbiome

Review: The microbiome of bat guano: for what is this knowledge important? – Dimkić et al. – Applied Microbiology and Biotechnology

Tick microbiomes in neotropical forest fragments are best explained by tick-associated and environmental factors rather than host blood source – Kueneman et al. – Microbial Ecology

Plant, root, and soil microbiome

Survival rates of microbial communities from livestock waste to soils: a comparison between compost and digestate – Akari and Uchida – Applied and Environmental Soil Science

Year, location, and variety impact on grape-, soil-, and leaf-associated fungal microbiota of Arkansas-grown table grapes – Cureau et al. – Microbial Ecology

Preprint: Agricultural fertilization with poultry manure results in persistent environmental contamination with the pathogen Clostridioides difficile – Frentrup et al. – bioRxiv

Impacts of invasive Australian Acacias on soil bacterial community composition, microbial enzymatic activities, and nutrient availability in Fynbos soils – Keet et al. – Microbial Ecology

A novel carboxylesterase derived from a compost metagenome exhibiting high stability and activity towards high salinity – Lu and Daniel – Genes

A two-year field study of nickel-agromining using Odontarrhena chalcidica co-cropped with a legume on an ultramafic soil: temporal variation in plant biomass, nickel yields and taxonomic and bacterial functional diversity – Saad et al. – Plant and Soil

Bacterial response to soil property changes caused by wood ash from wildfire in forest soils around mining areas: Relevance of bacterial community composition, carbon and nitrogen cycling – Zhang et al. – Journal of Hazardous Materials

Water and extremophile microbiome

Microcystis blooms aggravate the diurnal alternation of nitrification and nitrate reduction in the water column in Lake Taihu – Chen et al. – Science of the Total Environment

Temperature and microbial interactions drive the deterministic assembly processes in sediments of hot springs – He et al. – Science of the Total Environment

Cadmium sulfide nanoparticle biomineralization and biofilm formation mediate cadmium resistance of the deep‐sea bacterium Pseudoalteromonas sp. MT33b – Ma and Sun – Environmental Microbiology Reports

Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession – Shabarova et al. – Nature Microbiology

Built environment

Preprint: Half-life of biodegradable plastics in the marine environment depends on material, habitat, and climate zone – Lott et al. – bioRxiv

Water flushing irremovable biofilms on support material in dynamic membrane bioreactor: formation, composition, and microbial community – Huang et al. – Chemosphere

Phages and viruses

Preprint: Rampant prophage movement among transient competitors drives rapid adaptation during infection – Marshall et al. – bioRxiv

January 26, 2021

Review articles on hygiene hypothesis and COVID, role of microbiome in cancer, different studies on efficacy of probiotics in inflammatory and metabolic diseases, and many more…

General microbiome

The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome – B. Brett Finlay – PNAS

Exploring the Role of Gut Microbiome in Colon Cancer – Indranil Chattopadhyay – Applied Biochemistry and Biotechnology

Cancer trigger or remedy: two faces of the human microbiome – Anna Grenda – Applied Microbiology and Biotechnology

Human microbiome

Microbiota, Epigenetics and Trained Immunity: Convergent Drivers and Mediators of the Asthma Trajectory from Pregnancy to Childhood – Susan V Lynch – American Journal of Respiratory and Critical Care Medicine

Gut Microbial Signature of Hepatocellular Cancer in Men with Cirrhosis – Somaya Albhaisi – Liver Transplantation

An Evaluation of the Fecal Microbiome in Lynch Syndrome – Adalberto Gonzalez – Journal of Gastrointestinal Cancer

Gut microbiota condition the therapeutic efficacy of trastuzumab in HER2-positive breast cancer – Martina Di Modica – Cancer Research

Recent, mid-, and late-adulthood antibiotic use are associated with subsequent risk of diverticulitis – Long H.Nguyen – Gastroenterology

Animal microbiome

Gestational gut microbial remodeling is impaired in a rat model of preeclampsia superimposed on chronic hypertension – Jeanne A Ishimwe – Physiological Genomics

Diet, habitat environment and lifestyle conversion affect the gut microbiomes of giant pandas – Leijin – Science of the Total Environment

Functional Foods

Probiotic Lactobacillus casei Shirota prevents acute liver injury by reshaping the gut microbiota to alleviate excessive inflammation and metabolic disorders – Ren Yan – Microbial Biotechnology

Functional characterization and immunomodulatory properties of Lactobacillus helveticus strains isolated from Italian hard cheeses – Miriam Zago – PlosOne

The Acid-Dependent and Independent Effects of Lactobacillus acidophilus CL1285, Lacticaseibacillus casei LBC80R, and Lacticaseibacillus rhamnosus CLR2 on Clostridioides difficile R20291 – Sathursha Gunaratnam – Probiotics and Antimicrobial Proteins

Polyphosphate, Derived from Lactobacillus brevis, Modulates the Intestinal Microbiome and Attenuates Acute Pancreatitis – Shuhei Takauji – Digestive Diseases and Sciences

Human Intestinal Barrier: Effects of Stressors, Diet, Prebiotics, and Probiotics – Michael Camilleri – Clinical and Translational Gastroenterology

Plant, root and soil microbiome

Insights into the plant responses to drought and decoding the potential of root associated microbiome for inducing drought tolerance – Piyush Mathur – Physiologia Plantarum

Water microbiome

A genomic view of the microbiome of coral reef demosponges – S. J. Robbins – ISME Journal

Microbes in news

Gut Bacteria Offer Insight into Molecules Protective Against Asthma and COVID-19 – Biospace

January 18, 2021

Today’s articles primarily focus on the human gut microbiome, with one paper finding that artificial sweeteners may not be as bad for the gut as we think, and a link between the gut microbiome and chronic kidney disease by Yang et al. Another great paper also involved the use of biocontrol strains in plants to reduce wheat disease. Enjoy!

Human gut microbiome

Settlers of our inner surface – Factors shaping the gut microbiota from birth to toddlerhood. Laursen et al. FEMS Microbiology Reviews

Synbiotics alleviate the Gut Indole Load and Dysbiosis in Chronic Kidney Disease. Yang et al. Cells.

Effects of Transanal Irrigation on Gut Microbiota in Pediatric
Patients with Spina Bifida.
Furuta et al. Journal of Clinical Medicine.

High-dose saccharin supplementation does not induce gut microbiota changes or glucose intolerance in healthy humans and mice. Joan Serrano et al. Microbiome.

[Preprint] Listeria monocytogenes faecal carriage is common and driven by microbiota. Marc Garcia-Garceca et al. Bioxriv.

Modelling the effect of birth and feeding modes on the development of human gut microbiota. Xiong et al. Proceedings of the Royal Society b.

Gut microbiome partially mediates and coordinates the effects of genetics on anxiety-like behavior in Collaborative Cross mice. Jin et al. Scientific reports.

Plant, root and soil microbiome

Biocontrol of Two Bacterial Inoculant Strains and Their Effects on the Rhizosphere Microbial Community of Field-Grown Wheat. Wang et al. BioMed Research International


[preprint] Utilizing the Food-Pathogen Metabolome to Putatively Identify Biomarkers for the Detection of Shiga Toxin-Producing E. coli (STEC) from Spinach. Jadhav et al. Preprints.

A semi-tryptic peptide centric metaproteomic mining approach and its potential utility in capturing signatures of gut microbial proteolysis. Yan et al. Microbiome.

January 14, 2021

Greetings from Pittsburgh!

Today’s digest contains lots of microbial ecology articles focused on everything from the impacts of sleep on dental biofilm to the response of soil microbiota to high petroleum pollution. Also included are two articles focused on insect-plant interactions, with the first focusing on gall induction in insects and the second on the intestinal microbiota of the pine defoliator C. chuxiongica.

General microbiome

Novel cyanotoxin-producing Synechococcus in tropical lakes – Yew-Hoong et al. – Water Research

Multi-site human microbiome

Impacts of sleep on the characteristics of dental biofilm – Sotozono et al. – Scientific Reports

Animal experiments

Dysbiosis of rat vagina is efficiently rescued by the vaginal microbiota transplantation or probiotic combination: Vaginal microbiota transplantation rescues dysbiosis in rat vagina – Chen et al. – International Journal of Antimicrobial Agents

Are bacterial symbionts associated with gall induction in insects? – Hammer et al. – Arthropod-Plant Interactions

The diversity and function of intestinal microorganisms in four geographic Cephalcia chuxiongica (a pine defoliator) populations – Yu et al. – Journal of Applied Entomology

Animal microbiome

Linking bacterial communities associated with the environment and the ecosystem engineer Orchestia gammarellus at contrasting salt marsh elevations – Hernández et al. – Microbial Ecology

Plant, root, and soil microbiome

Response of bacterial and fungal communities to high petroleum pollution in different soils – Galitskaya et al. – Scientific Reports

Enzyme additives influence bacterial communities of Medicago sativa silage as determined by Illumina sequencing – Hu et al. – AMB Express

First reported quantitative microbiota in different livestock manures used as organic fertilizers in the Northeast of Thailand – Wongsaroj et al. – Scientific Reports

Water and extremophile microbiome

Coastal bacterial community response to glacier melting in the Western Antarctic Peninsula – Alcamán-Arias et al. – Microorganisms

Microbial necromass formation, enzyme activities and community structure in two alpine elevation gradients with different bedrock types – Bhople et al. – Geoderma

Exploring the taxonomical and functional profile of As Burgas hot spring focusing on thermostable β-galactosidases – DeCastro et al. – Scientific Reports

The effect of an adsorbent matrix on recovery of microorganisms from hydrocarbon-contaminated groundwater – Taylor et al. – Microorganisms

Built environment

Electrochemical performance and response of bacterial community during phenanthrene degradation in single-chamber air-cathode microbial fuel cells – Hua et al. – Environmental Science and Pollution Research

Food microbiology

Combination of Flos Sophorae and chili pepper as a nitrite alternative improves the antioxidant, microbial communities and quality traits in Chinese sausages – Tang et al. – Food Research International