Tag Archives: microbiome

December 14, 2021

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Today’s digest contains several great recent papers, but in particular I’d like to highlight a Nature Methods paper on applying network biology approaches to the microbiome, and a Nature paper which disentangles the effects of drugs and disease on host and microbiome.

General microbiome

Fast and flexible analysis of linked microbiome data with mako – Röttjers & Faust – Nature Methods. 

Combinatorial, additive and dose-dependent drug–microbiome associations – Forslund et al. Nature 

Mammalian gut metabolomes mirror microbiome composition and host phylogeny – Gregor et al. – ISME 

Human gut microbiome

Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity – Wang et al. – Genome Biology

Signature changes in gut microbiome are associated with increased susceptibility to HIV-1 infection in MSM – Chen et al.  – Microbiome

Cognitive behavioral therapy for irritable bowel syndrome induces bidirectional alterations in the brain-gut-microbiome axis associated with gastrointestinal symptom improvement – Jacobs et al. – Microbiome. 

Human oral microbiome

Impact of sleep on the microbiome of oral biofilms – Sotozono et al. – PLOS One

Functional screening of a human saliva metagenomic DNA reveal novel resistance genes against sodium hypochlorite and chlorhexidine – Wigand et al. BMC Oral Health

Animal Experiments

The immunotoxicity, but not anti-tumor efficacy, of anti-CD40 and anti-CD137 immunotherapies is dependent on the gut microbiota – Blake et al. – Cell Reports Medicine

Colonization of gut microbiota by plasmid-carrying bacteria is facilitated by evolutionary adaptation to antibiotic treatment – Zhang et al. – ISME

Sexual dimorphism in glucose metabolism is shaped by androgen-driven gut microbiome – Gao et al. – Nature Communications

December 4, 2021

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Human and General Microbiome

Multivariate associative patterns between the gut microbiota and large-scale brain network connectivity – N Kohn – Gut Microbes

Cervicovaginal levels of human beta defensins during bacterial vaginosis – Nathalia Mayumi Noda-Nicolau – PloS ONE

Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health – Francesco Marabita – Cell Systems

A specific structure and high richness characterize intestinal microbiota of HIV-exposed seronegative individuals – Tulio J Lopera – PloS ONE

Central role of intestinal epithelial glucocorticoid receptor in alcohol- and corticosterone-induced gut permeability and systemic response – Pradeep K Shukla – The FASEB Journal

Proof-of-principle demonstration of endogenous circadian system and circadian misalignment effects on human oral microbiota – Sarah L Chellappa – The FASEB Journal

Gender Variations in the Oral Microbiomes of Elderly Patients with Initial Periodontitis – Jie Zhao – Journal of Immunology Research

Characterization of Esophageal Microbiota in Patients With Esophagitis and Esophageal Squamous Cell Carcinoma – Zongdan Jiang – Frontiers in Cellular and Infection Microbiology

Gender-Specific Differences in Gut Microbiota Composition Associated with Microbial Metabolites for Patients with Acne Vulgaris – Yukun Huang – Annals of Dermatology

Gut microbiota develop towards an adult profile in a sex-specific manner during puberty – Katri Korpela – Scientific Reports

Gut microbiota-driven brain Aβ amyloidosis in mice requires microglia – Hemraj B Dodiya – The Journal of Experimental Medicine

Associations of the oral microbiota and Candida with taste, smell, appetite and undernutrition in older adults – Kristina S Fluitman – Scientific Reports

Altered cervicovaginal microbiota in premenopausal ovarian cancer patients – Asuka Morikawa – Gene

Social overcrowding impacts gut microbiota, promoting stress, inflammation, and dysglycemia – Clara Delaroque – Gut Microbes

Research Highlight: Gut microbiome and autism spectrum disorder – Eleni Kotsiliti – Nature Reviews Gastroenterology & Hepatology

Human and General Microbiome (Reviews)

Metagenomics studies for the diagnosis and treatment of prostate cancer – Ali Zarei – The Prostate

Regulation of common neurological disorders by gut microbial metabolites – Jeongho Park – Experimental & Molecular Medicine

The gut microbiota in retinal diseases – Marie-Agnès Bringer – Experimental Eye Research

Microbe-based management for colorectal cancer – Zi-Yun Gao – Chinese Medical Journal

Novel Strategies for Inhibition of Bacterial Biofilm in Chronic Rhinosinusitis – Aref Shariati – Journal of Applied Microbiology

Regulation of para-cresol production in Clostridioides difficile – Mark A Harrison – Current Opinion in Microbiology

Animal Microbiome (Non-Models)

Gut microbiome and metabolome in a non-human primate model of chronic excessive alcohol drinking – Daria Piacentino – Translational Psychiatry

A holobiont view of island biogeography: unraveling patterns driving the nascent diversification of a Hawaiian spider and its microbial associates – Ellie E Armstrong – Molecular Ecology

Interactions of Muscovy duck reovirus, gut microbiota, and host innate immunity: Transcriptome and gut microbiota analysis – Zheng Zhu – Veterinary Microbiology

Antibiotics, antibiotic resistance genes and microbial community in grouper mariculture – Lu-Xi He – The Science of the Total Environment

Beneficial Microbes and Compounds

Lactobacillus alleviated obesity induced by high-fat diet in mice – Wei Song – Journal of Food Science

Effect of prophylactic dextrose gel on the neonatal gut microbiome – Sophie L St Clair – Archives of Disease in Childhood

Polydextrose with and without Bifidobacterium animalis ssp. lactis 420 drives the prevalence of Akkermansia and improves liver health in a multi-compartmental obesogenic mice study – Christian Clement Yde – PloS ONE

Review: Studies and Application of Sialylated Milk Components on Regulating Neonatal Gut Microbiota and Health – Yushuang Wang – Frontiers in Nutrition

Environmental Microbiome

The highly diverse Antarctic Peninsula soil microbiota as a source of novel resistance genes – Andrés E Marcoleta – The Science of the Total Environment

Other Microbiomes

In vitro interaction network of a synthetic gut bacterial community – Anna S Weiss – The ISME Journal

Plant and Fungi Microbiome

Tryptophan metabolism and bacterial commensals prevent fungal dysbiosis in Arabidopsis roots – Katarzyna W Wolinska – PNAS

An ancient antimicrobial protein co-opted by a fungal plant pathogen for in planta mycobiome manipulation – Nick C Snelders – PNAS

Seed inhabiting bacterial endophytes of maize promote seedling establishment and provide protection against fungal disease – Gaurav Pal – Microbiological Research

November 20, 2021

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Highlights!

Review: Reporting guidelines for human microbiome research: the STORMS checklist – Chloe Mirzayi – Nature Medicine → The following article “provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results”

Honey bee genetics shape the strain-level structure of gut microbiota in social transmission – Jiaqiang Wu – Microbiome → “Our results indicated that host genetics influence the bee gut composition and suggest a gut-brain connection implicated in the gut bacterial strain preference”

Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples – Seesandra V Rajagopala – Cell Reports Methods → This study reports a method to study virome and microbiome of clinically relevant respiratory samples, using a children cohort. 

Human and General Microbiome

Response of Lung Microbiota to Changes of Pulmonary Innate Immunity Under Healthy Conditions – Taro Yasuma – American Journal of Respiratory and Critical Care Medicine

Small intestinal bacterial overgrowth in Alzheimer’s disease – Karol Kowalski – Journal of Neural Transmission 

Periodontitis Salivary Microbiota Worsens Colitis – J Qian – Journal of Dental Research

The Effects of Moderate Alcohol Consumption on Circulating Metabolites and Gut Microbiota in Patients With Coronary Artery Disease – Xinyue Zhao – Frontiers in Cardiovascular Medicine

Integrative Analysis of LGR5/6 Gene Variants, Gut Microbiota Composition and Osteoporosis Risk in Elderly Population – Dong-Sheng Di – Frontiers in Microbiology

Comparison of the Gut Microbiota in Patients with Benign and Malignant Breast Tumors: A Pilot Study – Peidong Yang – Evolutionary Bioinformatics Online

Temporal variability in quantitative human gut microbiome profiles and implications for clinical research – Doris Vandeputte – Nature Communications

Association between Parkinson’s disease and the faecal eukaryotic microbiota – Severin Weis – NPJ Parkinson’s Disease

Micronutrient supplements can promote disruptive protozoan and fungal communities in the developing infant gut – Ana Popovic – Nature Communications

An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness – Andrea Marfil-Sánchez – Gut Microbes

Efficacy and Outcomes of Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection in Children with Inflammatory Bowel Disease – Maribeth R Nicholson – Journal of Crohn’s & Colitis

The anti-inflammatory effect of bacterial short chain fatty acids is partially mediated by endocannabinoids – Amrita Vijay – Gut Microbes

Human and General Microbiome – Reviews

Bile acids as regulatory molecules and potential targets in metabolic diseases – Ai-Jin Xie – Life Sciences

Renaissance for Phage-Based Bacterial Control – Cory Schwarz – Environmental Science & Technology

Sulphur metabolism in colon cancer tissues: a case report and literature review – Hironori Fukuoka – The Journal of International Medical Research

Dietary fatty acids in gut health: Absorption, metabolism and function – E Xu – Animal Nutrition

The search for aliens within us: a review of evidence and theory regarding the foetal microbiome – Richard Cariño III – Critical Reviews in Microbiology

Human immune diversity: from evolution to modernity – Adrian Liston – Nature Immunology 

Beneficial Microbes and Compounds

Review: Human Milk Oligosaccharides as a Missing Piece in Combating Nutritional Issues during Exclusive Breastfeeding – Verawati Sudarma – Pediatric Gastroenterology, Hepatology & Nutrition

Review: Advancements in the Pharmaceutical Applications of Probiotics: Dosage Forms and Formulation Technology – Kshitis Chandra Baral – International Journal of Nanomedicine

Lactobacillus rhamnosus strain LRH05 intervention ameliorated body weight gain and adipose inflammation via modulating the gut microbiota in high-fat diet-induced obese mice – Yung-Tsung Chen – Molecular Nutrition & Food Research

Bifidobacterium infantis Maintains Genome Stability in Ulcerative Colitis via Regulating Anaphase-Promoting Complex Subunit 7 – Taotao Han – Frontiers in Microbiology

Galacto-oligosaccharide Supplementation Modulates Pathogen-Commensal Competition between Streptococcus agalactiae and Streptococcus salivarius – Rebecca E Moore – Chembiochem

Animal Microbiome (Non-models)

Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes – Yuqing Feng – Communications Biology

Contrasting microbiome dynamics of putative denitrifying bacteria in two octocoral species exposed to dissolved organic carbon (DOC) and warming – Nan Xiang – Applied and Environmental Microbiology

Plant Microbiome

Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis – Nan Yang – NPJ Biofilms and Microbiomes

Drops join to make a stream: high-throughput nanoscale cultivation to grasp the lettuce root microbiome – Antoine Persyn – Environmental Microbiology Reports

Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition – Alba Pacheco-Moreno – eLife

Small-scale agricultural grassland management can affect soil fungal community structure as much as continental scale geographic patterns – A Fox – FEMS Microbiology Ecology

Geographic and position-based variations in phyllospheric bacterial communities present on flue-cured tobacco – Jianbin Ye – Applied Microbiology and Biotechnology

Other Microbes

Improved quantitative microbiome profiling for environmental antibiotic resistance surveillance – Amelie Ott – Environmental Microbiome

Sediment Microbiota in Response to Circuitry of Sediment Microbial Fuel Cells, Revealed by 16S rRNA Gene Amplicon Sequencing – Yasuyuki Takemura – Microbiology Resource Announcements

Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate – Hyungseok Kim – The ISME Journal

Review: Microbial ecology of tourist Paleolithic caves – Zelia Bontemps – The Science of the Total Environment

Microbiome Analysis and Bioinformatics

Multivariate statistical monitoring system for microbial population dynamics – Koji Ishiya – Physical Biology

GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison – Die Dai – Nucleic Acids Research

metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes – Thea Van Rossum – Bioinformatics

Assessing saliva microbiome collection and processing methods – Abigail J S Armstrong – NPJ Biofilms and Microbiomes

Analysing microbiome intervention design studies: Comparison of alternative multivariate statistical methods – Maryia Khomich – PloS ONE

Technical note: overcoming host contamination in bovine vaginal metagenomic samples with Nanopore adaptive sequencing – Chian Teng Ong – Journal of Animal Science

Mian: Interactive Web-Based Microbiome Data Table Visualization and Machine Learning Platform – Boyang Tom Jin – Bioinformatics

September 15, 2021

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Today’s digest is fairly light. It includes an article focused on the protective role of bacterial endosymbionts on soil fungus, a preprint on the indoor environment as a source for human-associated anaerobes, and work demonstrating how protein biosensors can be used to track the effects osmotic stress on cells.

Happy reading!

General microbiome

Preprint: Comprehensive comparative genomics analysis for the emerging human pathogen Streptococcus dysgalactiae subsp. equisimilis (SDSE): A case study and Pan-subspecies genomic analysis – Saeb & Tayeb – bioRxiv

Preprint: The model arbuscular mycorrhizal fungus Rhizophagus irregularis harbours endosymbiotic bacteria with a highly reduce genome – Savary et al. – bioRxiv

Preprint: A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare? – van Vilet et al. – bioRxiv

Animal microbiome (for animals in the wild)

Differences in gut microbiome composition between sympatric wild and allopatric laboratory populations of omnivorous cockroaches – Tinker et al. – Frontiers in Microbiology

Plant, root, and soil microbiome

Bacterial endosymbionts protect beneficial soil fungus from nematode attack – Büttner et al. – Proceedings of the National Academy of Sciences of the United States of America

Built environment

Preprint: The indoor environment – A potential source for intact human-associated anaerobes – Pausan et al. – bioRxiv

Techniques

Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells – Cuevas-Velazquez et al. – Nature Communications

Microbiome and COVID19: some research highlights

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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)

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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

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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

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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

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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 Treatment – Cancers (MDPI)

Review: Influence of Resveratrol on the Cardiovascular Health Effects of Chronic Kidney Disease – International 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

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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