Microbiome and COVID19: some research highlights

Page created on June 20, 2021

Last update: July 4, 2021

The following quote from the translated abstract of the article Management Of COVID-19: The Zhejiang Experience Kaijin Xu et al., from the Journal Of Zhejiang University, mentioned:

Some patients with COVID-19 showed intestinal microbial dysbiosis with decreased probiotics such as Lactobacillus and Bifidobacterium, so nutritional and gastrointestinal function should be assessed for all patients. Nutritional support and application of prebiotics or probiotics were suggested to regulate the balance of intestinal microbiota and reduce the risk of secondary infection due to bacterial translocation.

As far as we could found, this text is the first report (published in the first half of May 2020) mentioning the influence of COVID19 on the gut microbiome composition. More information has been published in recent months about the links between this pandemic and the microbiome. This search included not only the respiratory microbiome but also those communities from the gut. 

In this post, we present a list of remarkable papers covering connections between microbiome and COVID19. If you have more suggestions, please tell us in the comments.

General and Respiratory Tract Microbiome

Metatranscriptomic Characterization Of COVID-19 Identified A Host Transcriptional Classifier Associated With Immune Signaling –  Haocheng Zhang – Clinical Infectious Diseases (published in May 2020)

The Lung Tissue Microbiota Features Of 20 Deceased Patients With COVID-19 – Jun Fan – The Journal Of Infection  (published in June 2020)

Nasopharyngeal Microbiota Profiling Of SARS-CoV-2 Infected Patients – Flavio De Maio- Biological Procedures Online (published in July 2020)

Metagenomic Next-Generation Sequencing Of Nasopharyngeal Specimens Collected From Confirmed and Suspect COVID-19 Patients – Heba H Mostafa – mBio  (published in November 2020)

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment – Jeremiah J. Minich – Microbiome (published in January 2021)

Variability In Digestive And Respiratory Tract Ace2 expression Is associated with the microbiome – Sean T Koester – PloS One (published in March 2021)

Functional Profiling Of COVID-19 Respiratory Tract Microbiomes – Niina Haiminen – Scientific Reports (published in March 2021)

Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19 – Maria Paz Ventero – Frontiers in Microbiology (Published in March, 2021)

Preprint: Signatures Of COVID-19 Severity And Immune Response In The Respiratory Tract microbiome – Carter Merenstein – MedRxiv (available from April 2021)

Preprint: Plasma Microbiome In COVID-19 Subjects: An Indicator Of Gut Barrier Defects And dysbiosis – Ram Prasad – BioRxiv (available from April 2021)

Evaluation Of Superinfection, Antimicrobial Usage, And Airway Microbiome With metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai – Qing Miao – Journal Of Microbiology, Immunology, And Infection (published in April 2021)

COVID-19 Influences Lung Microbiota Dynamics And Favors The Emergence Of Rare infectious diseases: A case report of Hafnia alvei pneumonia – Salvatore Lucio Cutuli – Journal Of Critical Care (published in April 2021)

The Lower Respiratory Tract Microbiome Of Critically Ill Patients With COVID-19 – Paolo Gaibani – Scientific Reports (available in May 2021)

Metagenomic Analysis Reveals Oropharyngeal Microbiota Alterations In Patients With COVID-19 –  Shengli Ma – Signal Transduction And Targeted Therapy (available in May 2021)

Preprint: Acute SARS-CoV-2 Infection Is Associated With An Expansion Of Bacteria Pathogens In the nose including Pseudomonas aeruginosa – Nicholas S Rhoades – BioRxiv (available from May 2021)

Nasopharyngeal Microbiota In SARS-CoV-2 Positive And Negative Patients – Phillip A Engen – Biological Procedures Online (published in June 2021)

SARS-CoV-2 Detection Status Associates With Bacterial Community Composition In patients and the hospital environment – Clarisse Marotz – Microbiome (published in June 2021)

Gut Microbiome studies

Gnotobiotic Rats Reveal That Gut Microbiota Regulates Colonic MRNA Of Ace2, The Receptor for SARS-CoV-2 Infectivity – Tao Yang- Hypertension (Published in May 2020)

Alterations In Gut Microbiota Of Patients With COVID-19 During Time Of Hospitalization – Tao Zuo – Gastroenterology (Published in May 2020)

Alterations In Fecal Fungal Microbiome Of Patients With COVID-19 During Time Of Hospitalization until Discharge – Tao Zuo – Gastroenterology (published in June 2020)

Maintaining standard volumes, efficacy and safety, of fecal microbiota transplantation for C. difficile infection during the COVID-19 pandemic: A prospective cohort study – Gianluca Ianiro – Digestive and Liver Diseases (Published in September 2020)

Gut Microbiota Composition Reflects Disease Severity And Dysfunctional Immune responses in patients with COVID-19 – Yun Kit Yeoh – Gut (published in January 2021)

The Faecal Metabolome In COVID-19 Patients Is Altered And Associated With Clinical features and gut microbes – Longxian Lv – Analytica Chimica Acta (published in January 2021)

The Intestinal And Oral Microbiomes Are Robust Predictors Of Covid-19 Severity The Main Predictor Of COVID-19-related Fatality – Doyle V. Ward – MedRxiv (available from Jan 2021)

16S rRNA Gene Sequencing Of Rectal Swab In Patients Affected By COVID-19 – Antonio Mazzarelli – PloS One (published in February 2021)

Investigation Of Nasal/Oropharyngeal Microbial Community Of COVID-19 Patients By 16S rDNA Sequencing – Martina Rueca – International Journal Of Environmental Research And Public Health (published in February 2021)

Integrated Gut Virome And Bacteriome Dynamics In COVID-19 Patients – Jiabao Cao – Gut Microbes  (published in March 2021)

Six-month Follow-up Of Gut Microbiota Richness In Patients With COVID-19 – Yanfei Chen – Gut (published in April 2021)

Gut Mycobiota Alterations In Patients With COVID-19 And H1N1 Infections And Their associations with clinical features – Longxian Lv – Communications Biology (published in April 2021)

Gut Microbiome And Resistome Changes During The First Wave Of The COVID-19 Pandemic in comparison with pre-pandemic travel-related changes – Ye Peng – Journal Of Travel Medicine (published in May 2021)

Gut microbiota, inflammation and molecular signatures of host response to infection – Wanglong Gou – Journal of Genetics and Genomics (published in May 2021)

Gut Microbiota May Not Be Fully Restored In Recovered COVID-19 Patients After 3-Month Recovery – Yu Tian – Frontiers In Nutrition (published in May 2021)

Gut Microbiome Composition Is Associated With COVID-19 Disease Severity – Pooja Patel – Gastroenterology  (published in May 2021)

The Gut Microbiome Of COVID-19 Recovered Patients Returns To Uninfected Status In A minority-dominated United States cohort – Rachel C Newsome – Gut Microbes (published in June 2021)

Reversion Of Gut Microbiota During The Recovery Phase In Patients With Asymptomatic or Mild COVID-19: Longitudinal Study  – Han-Na Kim – Microorganisms (published in June 2021)

Reviews, hypotheses, and other related topics

Divulgation post: Gut reaction: How the gut microbiome may influence the severity of COVID-19 – Shirin Moossavi and Marie-Claire Arrieta – The Conversation (June 21, 2020)

Intestinal Flora as a Potential Strategy to Fight SARS-CoV-2 Infection – Li-Hong He – Frontiers in Microbiology (Review; published in June 2020) 

Intestinal Permeability Changes With Bacterial Translocation As Key Events modulating systemic host immune response to SARS-CoV-2: A working hypothesis – Vincenzo Cardinale – Digestive And Liver Disease (published in September 2020)

The Potential Application Of Probiotics And Prebiotics For The Prevention And treatment of COVID-19 – Amin N Olaimat – NPJ Science Of Food (published in October 2020)

The Gut Microbiome: An Under-recognised Contributor To The COVID-19 Pandemic? – Jonathan P Segal – Therapeutic Advances In Gastroenterology  (published in November 2020)

Gut Microbiota in Covid-19: An unrecognised player? – Sabrina Donati Zeppa – Frontiers in Cellular and Infection Microbiology (Review, published in November 2020)

Is Gut Microbiota Dysbiosis A Predictor Of Increased Susceptibility To Poor Outcome of COVID-19 Patients? An Update – Carolina Ferreira – Microorganisms (published in December 2020)

Fecal microbiota transplantation for COVID-19; a potential emerging treatment strategy – Seyed Aria Nejadghaderi – Medical Hypotheses (Published in December 2020)

Do An Altered Gut Microbiota And An Associated Leaky Gut Affect COVID-19 Severity? – Heenam Stanley Kim – mBio (published in January 2021)

The Microbiome Of Bat Guano: For What Is This Knowledge Important? – Ivica Dimkić – Applied Microbiology And Biotechnology (published in January 2021)

Divulgation post: A healthy microbiome builds a strong immune system that could help defeat COVID-19 -Ana Maldonado-Contreras – The Conversation (January 22, 2021)

Microbiota Modulation Of The Gut-Lung Axis In COVID-19 – Gislane Lelis Vilela de Oliveira – Frontiers In Immunology (published in February 2021)

Next-Generation Sequencing Reveals The Progression Of COVID-19 – Xiaomin Chen – Frontiers In Cellular And Infection Microbiology (published in March 2021)

Metagenomics Approaches To Investigate The Gut Microbiome Of COVID-19 Patients – Sofia Sehli – Bioinformatics And Biology Insights (published in March 2021)

The Unique Impact of COVID-19 on Human Gut Microbiome Research – Ella Burchill – Frontiers in Medicine (Published in March 2021)

Review: Modulation Of Gut Microbiota For The Prevention And Treatment Of COVID-19 – Jiezhong Chen – Journal Of Clinical Medicine (Published in June 2021)

Acknowledgments

The author wants to thank Mauricio Morales (Undergraduate student; Universidad Mayor, Chile) for his help in the generation of this list.

Update (July 4, 2021). Thanks to MaximilianKohler and Rafael for their valuable suggestions for the list update.

Mycobiome (Early 2021 Semi-Annual Fungal Microbiome Picks)

It’s been a while, but its time to highlight some recent mycobiome articles!

Human mycobiome

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

Gut mycobiota in immunity and inflammatory disease – Li et al. – Immunity

Response to fungal dysbiosis by gut-resident CX3CR1(+) mononuclear phagocytes aggravates allergic airway disease.- Li et al. – Cell Host Microbe. 

Human anti-fungal Th17 immunity and pathology rely on cross-reactivity against Candida albicans. – Bacher et al. – Cell. 

Prevalence and diversity of filamentous fungi in the airways of cystic fibrosis patients – a Dutch, multicentre study. – Engle et al. – J Cyst Fibros.

Early gut mycobiota and mother-offspring transfer. – Schei – Microbiome

Fungi form interkingdom microbial communities in the primordial human gut that develop with gestational age. – Willis et al – FASEB J.

Investigating colonization of the healthy adult gastrointestinal tract by fungi. – Auchtung et al. – mSphere.

CX3CR1+ mononuclear phagocytes control immunity to intestinal fungi. – Leonardi et al. – Science.

Commensal Candida albicans positively calibrates systemic Th17 immunological responses. – Shao et al – Cell Host Microbe. 

Macrophages maintain epithelium integrity by limiting fungal product absorption. – Chikina et al. – Cell.

Fungal symbionts produce prostaglandin E2 to promote their intestinal colonization. – Tan et al. – Front Cell Infect Microbiol.

The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL. – Aykut et al – Nature. 

Fungal microbiota dysbiosis in IBD. – Sokol et al – Gut.

Malassezia is associated with Crohn’s disease and exacerbates colitis in mouse models. – Limon et al – Cell Host Microbe.

Macrophage interactions with fungi and bacteria in inflammatory bowel disease. – Leonardi et al. – Curr Opin Gastroenterol.

Fungi participate in the dysbiosis of gut microbiota in patients with primary sclerosing cholangitis. – Lemoinne et al – Gut

Intestinal fungi contribute to development of alcoholic liver disease. – Yang et al – J Clin Invest.

Animal mycobiome

The gut mycobiome of healthy mice is shaped by the environment and correlates with metabolic outcomes in response to diet – Mims and Al Abdallah et al. – Communications Biology

Profound mycobiome differences between segregated mouse colonies do not influence Th17 responses to a newly introduced gut fungal commensal. – Doron et al. – Fungal Genet Biol.

Season, age, and sex affect the fecal mycobiota of free-ranging Tibetan macaques (Macaca thibetana). – Sun et al – Am J Primatol.

Altered immunity of laboratory mice in the natural environment is associated with fungal colonization. – Yeung et al – Cell Host Microbe. 

Mycobiome techniques

The fungal frontier: a comparative analysis of methods used in the study of the human gut mycobiome. – Huseyin et al. – Front Microbiol. 

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics – Karen et al. – Microbiome

Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing – Lind et al – Microbiome

Tiara: Deep learning-based classification system for eukaryotic sequences –  Karlicki et al – bioRxiv.org

~ Kent Willis, MD

November 6, 2020

Shalom from Israel!

While the eyes of the world are looking at the US elections results, it’s good to know that the world of microbiome research is stable and produces great scientific discoveries. So stop refreshing the news websites, grab yourself a cup of cofee and enjoy your Saturday.

Today’s digest has some great papers about memory in microboimes, factors that shapes bacterial growth, infant skin microbial communities, degraded soils restoration using self-assembly communities, songbirds microbiome, antiSMASH3 is out (!), useful youtube video for metagenome ML analysis in MATLAB and more. Reminding those of you who are intrested in agriculture-related microbioe studies to stop by and follow my bot agmicroPapers

General microbiology

Memory shapes microbial populations, Chaitanya S Gokhale , bioRxiv

Bacterial–fungal interactions revealed by genome-wide analysis of bacterial mutant fitness, Emily C. Pierce, Nature Microbiology

Environmental and Physiological Factors Affecting High-Throughput Measurements of Bacterial Growth, Esha Atolia , mBio

Human microbiome

Host variables confound gut microbiota studies of human disease, Ivan Vujkovic-Cvijin, Nature

Infant Skin Bacterial Communities Vary by Skin Site and Infant
Age across Populations in Mexico and the United States
, Melissa B. Manus, mSystems

Plant and soil microbiome

Microbiome manipulation by a soil-borne fungal plant pathogen using effector proteins, Nick C. Snelders, Nature Plants

Assembly and variation of root-associated microbiota of rice during their vegetative growth phase with and without lindane pollutant, Jiayin Feng, Soil Ecology Letters

Restoring degraded microbiome function with self-assembled communities, Carlos Fernando Gutierrez Landazuri , FEMS Micro. Eco.

Multi-species relationships in legume roots: From pairwise legume-symbiont interactions to the plant – microbiome – soil continuum, Myrto Tsiknia, FEMS Micro. Eco.

Animal microbiome

Evidence supporting the microbiota–gut–brain axis in a songbird, Morgan C. Slevin, Biology Letters

Comparative Analysis of the Fecal Microbiota of Wild and Captive Beal’s Eyed Turtle (Sacalia bealei) by 16S rRNA Gene Sequencing, Jonathan J. Fong , Front. Micro.

High-Throughput Cultivation for the Selective Isolation of Acidobacteria From Termite Nests, Markus Oberpaul , Front. Micro.

Bioinformatics

EUKulele: Taxonomic annotation of the unsung
eukaryotic microbes
, Arianna I. Krinos, JOSS

The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes, Kai Blin, Nucleic Acids Research

**Youtube Video- Microbiome: How to Navigate Through Matlab to Perform Machine Learning Analysis on Metagenomics Data

**Help questionnaire! Natural Products – Data Repositories Questionnaire

September 20, 2020

Shalom from Israel and have a happy Jewish New Year!

As yesterday’s digest was packed with great papers, today’s post is a bit thinner- but still with great material. First, take a look at two virtual and fascinating events to be held in the next months. In addition, you’ll find a mini-review about molecular epidiomiology, locust-related microbiome, a fascinating research paper exploring the actual proportion of sequenced prokaryots and a even a paper focusing on the microbiome of hemp.

Stay healthy, wear a mask.

Events

LMU CAM Strategic Partnership Online Symposium: The role of microbes in plant health: Emerging topics!

ISME Virtual Microbial Ecology Summit

Human microbiome

Gut microbiota, NLR proteins, and intestinal homeostasis, Hao Guo, JEM

*Mini-review- Molecular epidemiology in current times, Burkhard Tummler, Env. Micro.

Animal microbiome

Microbiome-related aspects of locust density-dependent phase transition, Omer Levy, bioRxiv

Environmental microbiome

**Estimate of the sequenced proportion of the global prokaryotic genome, Zheng Zhang, Microbiome

Microbial dark matter filling the niche in hypersaline microbial mats, Hon Lun Wong, Microbiome

Pan‐genome study of Thermococcales reveals extensive genetic diversity and genetic evidence of thermophilic adaption, Chaofang Zhong , Env. Micro.

Plant microbiome

Evaluating the microbiome of hemp, Samuel E. Barnett, Phytobiomes

September 5, 2020

Have a nice weekend! Today, this Digest includes a good amount of reviews covering different topics (from the concept of inflammageing to the impact of the microbiome on cancer treatment), as well as a report covering the use of flow cytometry to search for microbiome markers in Crohn’s disease patients, and studies on microbiota and portal hypertension, the microbiome of pesticide-treated soils and the effect of natural microbes on hydrocarbon degradation.

Human and General Microbiome

Cytometric fingerprints of gut microbiota predict Crohn’s disease state –  Peter Rubbens – The ISME Journal

Review: Is inflammageing influenced by the microbiota in the aged gut? A systematic review – Cabirou M Shintouo – Experimental Gerontology

Review: The Gut Microbiome, Inflammation, and Salt-Sensitive Hypertension – Fernando Elijovich – Current Hypertension Reports 

Review: Intestinal microbial metabolites in human metabolism and type 2 diabetes – Hilde Herrema – Diabetologia

Review: Gut Microbiota Dysbiosis as a Target for Improved Post-Surgical Outcomes and Improved Patient Care. A Review of Current Literature – Fatema Mustansir Dawoodbhoy – Shock

Review: The Role of the Microbiome in Cancer and Therapy Efficacy: Focus on Lung Cancer – Adrienne Halley – Anticancer Research 

Review: Breast and Gut Microbiota Action Mechanisms in Breast Cancer Pathogenesis and TreatmentCancers (MDPI)

Review: Influence of Resveratrol on the Cardiovascular Health Effects of Chronic Kidney DiseaseInternational Journal of Molecular Sciences

Review: An RNA-centric view on gut Bacteroidetes – Daniel Ryan – Biological Chemistry

Exploratory Research on the Relationship between Human Gut Microbiota and Portal Hypertension – Keiji Yokoyama – Internal Medicine

Gut microbiome alterations in type 1 autoimmune pancreatitis after induction of remission by prednisolone – Ken Kamata – Clinical and Experimental Immunology

Type I IFNs and CD8 T cells increase intestinal barrier permeability after chronic viral infection – Lara Labarta-Bajo – Journal of Experimental Medicine

Plant-associated Microbiome

Prokaryotic and microeukaryotic communities in an experimental rice plantation under long-term use of pesticides – Maria Pilar Serbent – 

Environmental Microbiome

Effect of natural microbiome and culturable biosurfactants-producing bacterial consortia of freshwater lake on petroleum-hydrocarbon degradation – Irfan Ali Phulpoto – Science of The Total Environment

Animal Microbiome

Alterations in the gut-associated microbiota of juvenile Caribbean spiny lobsters Panulirus argus (Latreille, 1804) infected with PaV1 – Jesús Alejandro Zamora-Briseño – Journal of Invertebrate Pathology

Effects of Zinc Oxide and Arginine on the Intestinal Microbiota and Immune Status of Weaned Pigs Subjected to High Ambient Temperature – Se Young Yoon – Animals (MDPI)

The Microbiome of Neotropical Water Striders and Its Potential Role in Codiversification – Anakena M Castillo – Insects (MDPI)

Beneficial Microbes and Compounds

Effects of probiotic bacterium Weissella cibaria CMU on periodontal health and microbiota: a randomised, double-blind, placebo-controlled trial – Mi-Sun Kang – BMC Oral Health

Other

A 500-year tale of co-evolution, adaptation, and virulence: Helicobacter pylori in the Americas – Zilia Y Muñoz-Ramirez – The ISME Journal

August 26, 2020

Shalom from Israel! Today’s digest has some great review papers, as well as research articles focusing on citures disease, vaginal microbiome, gut virome and some cool bioinformatic tools.

Also, check out this great event for the soil microbilogists out there: Non-academic Careers in Soil Ecology: a virtual career panel, hosted by MSU.

Enjoy your summer holiday if you managed to get one and as always- find yourself the time to rest and re-energize.

General

**review: Compartmentalization drives the evolution of symbiotic cooperation, Guillaume Chomicki, Phil. Tran. B

Marine microbiomoe

Assessing the strength and sensitivity of the core microbiota approach on a highly diverse sponge reef, Carmen Astudillo-Garica , Env. Micro.

Plant microbiome

Cooperation, Competition, and Specialized Metabolism in a Simplified Root Nodule Microbiome, Bridget L. Hansen , mBio

Stable isotope informed genome-resolved metagenomics uncovers potential trophic interactions in rhizosphere soil, Evan P. Starr, bioRxiv

Disease-Induced Microbial Shifts in Citrus Indicate Microbiome-Derived Responses to Huanglongbing Across the Disease Severity Spectrum, Nichole A. Ginnan , Phytobiomes

Human microbiome and virome

Cervicovaginal Microbiome Composition Is Associated with Metabolic Profiles in Healthy Pregnancy, Andrew Oliver , mBio

The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut, Ann C. Gregory , Cell Host Microbe

Bioinformatics

BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters, Satria Kutsar, bioRxiv

**mini-review: Natural product discovery through microbial genome mining, Emma Kenshole, Cur. Op. Chem. Bio.

Available Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations, Murilo Henrique Anzolini Cassiano, mSystems

June 27, 2020

Shalom from Israel and a Happy world microbiome day!

Yes, it is a true day! celebrating the huge diversity of microbes around us, above us, below us and inside us. Check the day’s official website for more information, and take the weekend to appreciate this amazing field and your own personal contribution to advancing our knowledge about microbial communities on our planet.

Personally, I did my undergrad in Ecology and Evolution, confidence that I’ll my scientific career will focus on plant ecology and distribution, or at least large animals. Microbiology classes and introduction labs bored me, and I did my best to avoid this topic. But all of a sudden, during my Master’s degree (where I worked on a pathogenicity mechanism of postharvest disease-causing bacteria), I fell in love with microbiology in general, and specific bacterial communities. The huge untapped diversity, the unbelievable functions and the amazing interactions needed to maintain a functional community of these invisible inhabitants just fascinated me. Today, as a Ph.D. student exploring secondary metabolites gene clusters in soil and root microbiome, I’m a super-fan of the bacterial world.

How did you end up being microbiome suckers? Feel free to share your stories here as a comment, on MD FB page, or directly on tweeter.

Today’s digest include several microbimoe papers of animal midels (including ‘dirty mice’), diseased tomatoes taxonomical and functional microbiome profile, AND- a sweet reminder of the pre-COVID-19 world, with an analysis of the dust microbiome of a plane (remember this vehicle?).

Human and Animal Models microbiome

**Microbial transmission in animal social networks and the social microbiome, Amar Sarkar , Nat. Eco. Evo.

Does entry to center-based childcare affect gut microbial colonization in young infants?, Gerben D. A. Hermes, Scientific Reports

Serum metabolites reflecting gut microbiome
alpha diversity predict type 2 diabetes
, Cristina Menni, Gut microbes

**New Insights into the Immune System Using Dirty Mice, Sara E. Hamilton, J. Immunology.

Optimization of cerebrospinal fluid microbial metagenomic sequencing diagnostics,Josefin Olausson , bioRxiv

Sleep fragmentation increases blood pressure and is associated with alterations in the gut microbiome and fecal metabolome in rats, Katherine.Maki, Phys. Geno.

Animal microbiome

Environment Shapes the Microbiome of the Blue Orchard Bee, Osmia lignaria, Hamutahl Cohen, Microbial Ecology

The gut mycobiome of healthy mice is shaped by the environment and shapes metabolic outcomes in response to diet, Tahliyah S. Mims, bioRxiv

Microbial communities network analysis of anaerobic reactors fed with bovine and swine slurry, Eliane Cristina Gruszka Vendruscolo, Sci. Tot. Env.

Metagenomic analysis reveals significant differences in microbiome and metabolic profiles in the rumen of sheep fed low N diet with increased urea supplementation, Zhipeng Li, FEMS Micro. Eco.

Soil and Plant microbiome

Changes in Bacterial and Fungal Microbiomes Associated with Tomatoes of Healthy and Infected by Fusarium oxysporum f. sp. lycopersici, Xin Zhou, Microbial Ecology

Insights into drylands biocrust microbiome: geography, soil depth, and crust type affect biocrust microbial communities and networks in Mojave Desert, USA, Nuttapon Pombubpa, FEMS Micro. Eco.

Exploring the Lignin Catabolism Potential of Soil-Derived Lignocellulolytic Microbial Consortia by a Gene-Centric Metagenomic Approach, Laura Díaz-García, Microbial Ecology

Shotgun Metagenomics Of Dust Microbiome From Flight Deck And Cabin In Civil Aviation Aircraft, Yu Sun, Indoor Air

Bioinformatics

MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data, D.R. Finn , FEMS Micro. Eco.

June 12, 2020

Buenos dias and greetings from Spain!

Today we can announce a Virtual Skin Microbiome Symposium held by New York Society of Cosmetic Chemists (NYSCC), that will start on June 15 to June 22, 2020, will include five on-demand sessions, a live panel Q&A and the Suppliers’ Day Digital Pop-Up & Solutions Center.

COVID-19

Epidemiological models are important tools for guiding COVID-19 interventions – Robin N. Thompson – BMC Medicine

Diagnosis of COVID-19 in children: the story evolves – R. Harwood and I. Sinha – BMC Medicine

Africa’s response to COVID-19 – Chikwe Ihekweazu and Emmanuel Agogo – BMC Medicine

Evaluation of the potential incidence of COVID-19 and effectiveness of containment measures in Spain: a data-driven approach – Alberto Aleta and Yamir Moreno – BMC Medicine

Pre-print – Identification of unique mutations in SARS-CoV-2 strains isolated from India suggests its attenuated pathotype – Shubham Gaurav – bioRxiv

General microbiome

Feasibility of collection and analysis of microbiome data in a longitudinal randomized trial of community gardening – Mireia Gascon – Future microbiology

Targeted microbiome depletion – A Du ToitNature Reviews Microbiology

Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host D Gouveia et al. – Biofilms and Microbiomes

Microbiome factors in HPV-driven carcinogenesis and cancers D Lin et al. – Plos Pathogens

Human respiratory microbiome

Clinical diagnostic application of metagenomic next-generation sequencing in children with severe nonresponding pneumonia – Heping Wang – PLOS ONE

Human vaginal microbiome

Exploring potential of vaginal Lactobacillus isolates from South African women for enhancing treatment for bacterial vaginosis – Anna-Ursula Happel – PLOS ONE

Human nearly-sterile sites

Parapseudoflavitalea muciniphila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a human peritoneal tumour and reclassification of Pseudobacter ginsenosidimutans as Pseudoflavitalea ginsenosidimutans comb. nov. – Paul A. Lawson et al. – Microbiology society

Animal experiments

Evaluation of the bacterial ocular surface microbiome in ophthalmologically normal dogs prior to and following treatment with topical neomycin-polymyxin-bacitracin – Callie M Rogers et al. – PLOS ONE

Short-chain fructo-oligosaccharides supplementation to suckling piglets: Assessment of pre- and post-weaning performance and gut health – Miriam Ayuso – PLOS ONE

Polysaccharides isolated from Cordyceps Sinensis contribute to the progression of NASH by modifying the gut microbiota in mice fed a high-fat diet – Lei Chen et al. – PLOS ONE

Effect of dietary gossypol supplement on fermentation characteristics and bacterial diversity in the rumen of sheep – CaiDie Wang – PLOS ONE

Polysaccharides isolated from Cordyceps Sinensis contribute to the progression of NASH by modifying the gut microbiota in mice fed a high-fat diet – Lei Chen – PLOS ONE

β-glucan administration improves growth performance and gut health in New Zealand White and APRI rabbits with different breed responses – Mahmoud M Abo Ghanima – PLOS ONE

Comparative study of gut microbiota in Tibetan wild asses (Equus kiang) and domestic donkeys (Equus asinus) on the Qinghai-Tibet plateau – H Liu, X Zhao – PeerJ

Pre-print – Differential genes and microbiota revealed by serum metabolomics of obese rats after intervention by Rhizoma Coptidis – K Luo et al. – Research Square

Pre-print – Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria – Leeann Klassen et al. – bioRxiv

Animal microbiome

Characterizing the microbiome of ectoparasitic louse flies feeding on migratory raptors – Rebecca A McCabe et al. – PLOS ONE

Characterization of the microbiota of commercially-traded finfish fillets – HR Shehata et al. – Food Research International

A bug’s life-delving into the challenges of helminth microbiome studies – F Formenti et al. – PLoS Neglected Tropical Diseases

Fish skin and gut microbiomes show contrasting signatures of host species and habitat – FÉ Sylvain et al. – Applied and Environmental

Plant, root, and soil microbiome

Isolation, Screening and Identification of Free-Living Diazotrophic Bacteria from Salinated Arid Soils – SA Begmatova et al. – Microbiology

Eukaryotic Microbial Communities in Japanese Arable AndisolsInvestigated by Amplicon Sequencing of 18S rRNA – GenesKazumori Mise et al. – American Society for microbiology

Combined effects of green manure returning and addition of sewage sludge compost on plant growth and microorganism communities in gold tailings. – YJ Ai et al. – Environmental Science and Pollution

Taxonomic shifts in arbuscular mycorrhizal fungal communities with shade and soil nitrogen across conventionally managed and organic coffee agroecosystems. – L Aldrich-Wolfe et al. – Mycorrhiza

Metagenomics Framework for the study of Soil Microbial Communities Based 16s rRNA Gene profiling approach – A Basu et al. – International Journal of Biotechnology

Soil microbial communities in the rhizosphere of Robinia pseudoacacia L. after being exposed to elevated atmospheric CO2 and cadmium for 4 years – X Jia et al. – Applied Soil Ecology

Soil aggregates by design: Manufactured aggregates with defined microbial composition for interrogating microbial activities in soil microhabitats – HJ Harvey et al – Soil Biology and Biochemistry

Would fertilization history render the soil microbial communities and their activities more resistant to rainfall fluctuations? J Kátai et al. – biorxiv

Pre-print – Meta-transcriptomic detection of diverse and divergent RNA viruses in green and chlorarachniophyte algae – Justine Charon et al. – bioRxiv

Water and extremophile microbiome

Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of Qinhuangdao mariculture area – Shuping Wang et al. – PLOS ONE

Spatial dynamics of eukaryotic microbial communities in the German Bight – PAA Sprong et al. – Journal of Sea Research

Temporal distribution of microbial community in an industrial wastewater treatment system following crash and during recovery periods – H Barak et al. – Chemosphere

Pre-print – Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbiome structure and key drivers – Chenjing Jiang et al. – bioRxiv

Pre-print – Ozone nanobubble treatment effectively reduced pathogenic Gram positive and negative bacteria in freshwater and safe for tilapia – Chayuda Jhunkeaw et al. – bioRxiv

Pre-print – Impact of trimethoprim on the river microbiome and antimicrobial resistance. James Delaney et al. – bioRxiv

Bioinformatics

gutMEGA: a database of the human gut MEtaGenome Atlas – Q Zhang et al. – Briefings in Bioinformatics

June 09, 2020

Good morning everyone!

Today’s digest presents several antibiotic resistance papers, as well as hospital ICU microbiome study, a microbial nomenculture paper, bunch of human microbiome papers (both gut and vaginal), as well as two computational platforms for analyzing microbial data.

In a more personal note– recently, my PhD research (at ARO and The Hebrew U, Israel) resulted in two manuscripts dealing with the exciting world of bacterial secondary metabolites. The first one is a review paper where we present state-of-the-art tools and methodologies to study and identify novel secondary metabolites gene clusters within the widely diverse soil and root bacterial communities. We present a conceptual pipeline for an efficient use of these culture-based and culture-independent platforms to identify novel antimicrobials-producing gene clusters in-vivo.

The second one (a bioRxiv pre-print) utilized some of these techniques to explore differences in secondary metabolites gene clusters between soil and roots bacterial communities, in terms of diversity, composition and taxonomy. We then took advantage of this data and deeply focused on root-enriched and abundant sequences (those that were associated with NRPS and PKS, mega-enzymes that produces two very important families of secondary metabolites- nonribosomal peptides and polyketides). Then, we used a unique culture-independent platform (eSNaPD, from Sean Brady lab @ Rockefeller U, NY) and were able to actually recover 5 clones (~40Kb in length) that harbored five novel gene clusters. At least one of these probably encode for an antifungal metabolites (derived from Actinobacteria). This piepline/platform is applicable for other uses of course, depending on your research question and the functions you’re intrested in. I’ll be happy for any feedback regarding the bioRxiv MS (either directly there or via my tweeter).

General microbiology

Roadmap for naming uncultivated Archaea and Bacteria, Alison E. Murray, Nature Microbiology

Human microbiome

Re-evaluating the relationship between missing heritability and the microbiome, Gavin Douglas , Microbiome

Microbes and mental health: Can the microbiome help explain clinical heterogeneity in psychiatry?, Christina L. Hayes, Front. Neuroendocrinology

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations, Nicolai Karcher, Genome Biology

Exploring potential of vaginal Lactobacillus isolates from South African women for enhancing treatment for bacterial vaginosis, Anna Ursula Happel , PLOS Pathogens

Hospital microbiome

Temporal variations in bacterial community diversity and composition throughout intensive care unit renovations, Jessica Chopik , Microbiome

Antibiotic Resistance

The household resistome – frequency of beta-lactamases, class 1 integron and antibiotic resistant bacteria in the domestic environment, Laura S. Schages , bioRxiv

Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus, Henrique Machado, bioRxiv

Coexistence of Antibiotic Resistance Genes and Virulence Factors Deciphered by Large-Scale Complete Genome Analysis, Yu Pan, mSystems

Bioinformatics

A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems, Begum D. Topcuoglu, mBio

PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing, Alexis Robitaille, BMC Bioinformatics

February 28, 2020

Good morning/afternoon y’all! today’s digest features some interesting-to-read genral biotech and ecology papers, as weel as the first gene catalouge of the vaginal microbiome, American pets microbiome revealed, cool microbiome engineering for biocontrol purpose in agriculture, a bunch of salt- and sweet-water microbiome studies and more!

Have a great weekend! put the guilt aside and enjoy some time with your spouse, family, pets, hobbies and anything else that you enjoy!

General Science

is is a very cool paper, beuatifuly presenting the connection and applicatino of two very ‘hot’ topics in today biotechnology world- AI and drug discovery:A Deep Learning Approach to Antibiotic Discovery- A Deep Learning Approach to Antibiotic Discovery, Jonathan M. Stokes, Cell

** Novel Outlook in Microbial Ecology: Nonmutualistic Interspecies Electron Transfer, Roman Moscoviz, Trends in Microbiology

A solution to minimum sample size for regressions, David J. Jenkins , PLOS One

The relationship between the host genome, microbiome, and host phenotype, Harald Brussow, Env. Micro.

Human microbiome

** A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina, Bing Ma, Nature Communications

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention, Jessica A. Grembi, Sci. Rep.

Analysis of healthy reference ranges for clinically relevant gut microbial indicators: A large web-based cohort study in Japan, Satoshi Watanabe , bioRxiv

Short chain fatty acids produced by colonizing intestinal commensal bacterial interaction with expressed breast milk are anti-inflammatory in human immature enterocytes, Nan Zheng, PLOS One

Animal microbiome

Characterization of gut microbiomes of household pets in the United States using a direct-to-consumer approach, Aashish R. Jha, PLOS One

Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome, Samuel J. Bowers, PLOS One

Insect microbiome

**Engineering bacterial symbionts of nematodes improves biocontrol potential of the western corn rootworm, Ricardo A. R. Machado, Nature Biotechnology

Plant and soil microbiome

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome, Siwen Deng , bioRxiv

Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes, Yuting Liang , Env. Micro.

Network analysis infers the wilt pathogen invasion associated with non-detrimental bacteria, Qiolong Hu , npj biofims and microbiomes

Marine microbiome

Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings, Marcela Franca Dias, Water Research

Niche partitioning of methane-oxidizing bacteria along the oxygen–methane counter gradient of stratified lakes, Magdalena J. Mayr, ISME

A metagenomic assessment of microbial eukaryotic diversity in the global ocean, Aleix Obiol, Mol. Eco. Res.

Ocean acidification affects microbial community and invertebrate settlement on biofilms, Katie S. Nelson, Sci. Rep.

Understanding and creating biocementing beachrocks via biostimulation of indigenous microbial communities, Asha A. Ramachandran , Env. Biotech.