Category Archives: General Microbiome

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.

June 19, 2021

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Have a nice weekend (¡Tengan un muy buen fin de semana!) In this Digest, a set of papers released during this latter month were selected, covering some of the most remarkable articles for this week. Please, if you want to highlight another article, please suggest it in the comments.  

Events

NGLess tutorial for processing metagenomes – Big Data Biology Lab – June 25
Registration available (closing June 22) at: https://docs.google.com/forms/d/e/1FAIpQLSebHvVFknM4Sy3ztMQbwQVxJ441VgRjJDPgCAPD4opse4znhQ/viewform

Human and General Microbiome

The Bacterial Microbiota Of Hunner Lesion Interstitial Cystitis/Bladder Pain Syndrome – J Curtis Nickel – BJU International

Microbiome-encoded Bile Acid Metabolism Modulates Colonic Transit Times – Naisi Li – IScience

Psychobiotics For Patients With Chronic Gastrointestinal Disorders Having Anxiety Or Depression Symptoms – Viet Hang Dao – Journal Of Multidisciplinary Healthcare

Homeostasis Of Mucosal Glial Cells In Human Gut Is Independent Of Microbiota – Timna Inlender – Scientific Reports

Yearly Changes In The Composition Of Gut Microbiota In The Elderly, And The Effect of lactobacilli intake on these changes – Ryuta Amamoto – Scientific Reports

Don’t Worry, Heavy Moms; Just Eat Your Broccoli(or Kimchi)! Co-diet Of High-fiber and high-fat helps give birth to healthy offspring through gut microbiota-to-brain signaling –  Sun-Kyung Lee – Molecules And Cells

Dietary Fiber Intake, The Gut Microbiome, And Chronic Systemic Inflammation In A cohort of adult men – Wenjie Ma – Genome Medicine

Commentary: The Role Of The Microbiome In Inflammation During Tuberculosis – Anou M Somboro – EBioMedicine

Vaginal Bacterial Load In The Second Trimester Is Associated With Early Preterm birth recurrence: a nested case-control study – Laura Goodfellow – BJOG

Bacteria-Mediated Synergistic Cancer Therapy: Small Microbiome Has A Big Hope – Xinyu Lou – Nano-micro Letters

Spatial Heterogeneity Analysis Of The Human Virome With Taylor’s Power Law – Zhanshan Sam Ma – Computational And Structural Biotechnology Journal

The Influence Of Nutritional Factors On Immunological Outcomes – Evanthia Tourkochristou – Frontiers In Immunology

Gut Microbial SNPs Induced By High-Fiber Diet Dominate Nutrition Metabolism And Environmental Adaption of Faecalibacterium prausnitzii in Obese Children – Hui Li – Frontiers In Microbiology

Gut Microbiota Regulate Gut-Lung Axis Inflammatory Responses By Mediating ILC2 Compartmental Migration – Qinqin Pu – Journal Of Immunology

Effects Of Cat Ownership On The Gut Microbiota Of Owners – Guankui Du – PloS One

Effect Of COVID-19 Precautions On The Gut Microbiota And Nosocomial Infections – Armin Rashidi –  Gut Microbes

Association Between Oral Microflora And Gastrointestinal Tumors (Review)– Xiaoxiao Li – Oncology Reports

Bacteroides-dominant Gut Microbiome Of Late Infancy Is Associated With Enhanced neurodevelopment – Sukhpreet K Tamana – Gut Microbes

Proteome-wide Prediction Of Bacterial Carbohydrate-binding Proteins As A Tool For understanding commensal and pathogen colonisation of the vaginal microbiome – François Bonnardel  – NPJ Biofilms And Microbiomes

Investigating The Origin Of The Fetal Gut And Placenta Microbiome In Twins – Nayo Williams – The Journal Of Maternal-fetal & Neonatal Medicine

Levels Of Trimethylamine N-Oxide Remain Elevated Long Term After Left Ventricular Assist Device and Heart Transplantation and Are Independent From Measures of  Inflammation and Gut Dysbiosis – Melana Yuzefpolskaya – Circulation: Heart Failure

The Impact Of Device-assisted Therapies On The Gut Microbiome In Parkinson’s disease – Michal Lubomski – Journal Of Neurology

Alterations In Microbiome Composition And Metabolic Byproducts Drive Behavioral And transcriptional responses to morphine – Rebecca S Hofford – Neuropsychopharmacology

Structural Specificities Of Cell Surface Beta-glucan Polysaccharides Determine commensal yeast mediated immuno-modulatory activities – Changhon Lee – Nature Communications

Integrated Omics Endotyping Of Infants With Respiratory Syncytial Virus bronchiolitis and risk of childhood asthma – Yoshihiko Raita – Nature Communications

Fecal Short-chain Fatty Acids And Obesity In A Community-based Japanese Population: The DOSANCO Health Study – Ryodai Yamamura – Obesity Research & Clinical Practice

Anaerobic Microbiota Derived From The Upper Airways Impact Staphylococcus Aureus physiology –  Sarah K Lucas – Infection And Immunity

Review: A New Biological Triangle In Cancer: Intestinal Microbiota, Immune Checkpoint inhibitors and antibiotics – Jie Zhang – Clinical & Translational Oncology

The Microbiome And Gynecologic Cancer: Current Evidence And Future Opportunities – Laura M Chambers Current – Oncology Reports

Increased Bacterial Proteolytic Activity Detected Before Diagnosis Of Ulcerative Colitis – Heather J Galipeau – Inflammatory Bowel Diseases

Characterization Of An Alpha-glucosidase Enzyme Conserved In Gardnerella spp. Isolated from the human vaginal microbiome – Pashupati Bhandari – Journal Of Bacteriology

Catechin Metabolites Along With Curcumin Inhibit Proliferation And Induce Apoptosis in Cervical Cancer Cells by Regulating VEGF Expression In-Vitro – Elnaz Khojaste – Nutrition And Cancer

Review: The Lung Microbiome In Lung Transplantation – John E McGinniss – The Journal Of Heart And Lung Transplantation

Vaginal Microbiome: Normalcy Vs Dysbiosis – Viqar Sayeed Saraf – Archives Of Microbiology

Beneficial Microbes, Compounds and Interventions

Lactobacillus acidophilus LA14 Alleviates Liver Injury – Longxian Lv – mSystems

Desulfovibrio vulgaris, A Potent Acetic Acid-producing Bacterium, Attenuates nonalcoholic fatty liver disease in mice – Ying Hong – Gut Microbes

Review: The Interaction Of Akkermansia muciniphila With Host-derived Substances, Bacteria and diets – Tatsuro Hagi – Applied Microbiology And Biotechnology

Ganoderma lucidum Polysaccharide Modulates Gut Microbiota And Immune Cell Function to inhibit inflammation and tumorigenesis in colon – Cuiling Guo – Carbohydrate Polymers

The Outer Membrane Protein Amuc_1100 Of Akkermansia muciniphila Alleviates The depression-like behavior of depressed mice induced by chronic stress – Rongrong Cheng – Biochemical And Biophysical Research Communications

JianpiQinghua Granule Reduced PPI Dosage In Patients With Nonerosive Reflux Disease: A multicenter, randomized, double-blind, double-dummy, noninferiority study – Jiaqi Zhang –  Phytomedicine

Circadian Disruption-induced Metabolic Syndrome In Mice Is Ameliorated By Oat Beta-glucan mediated by gut microbiota – Wai-Yin Cheng – Carbohydrate Polymers

Effects Of Mediterranean Diet On Plasma Metabolites And Their Relationship With insulin resistance and gut microbiota composition in a crossover randomized clinical trial – Serena Galié – Clinical Nutrition

Calorie Restriction Conferred Improvement Effect On Long-term Rehabilitation Of ischemic stroke via gut microbiota– Jia-Ting Huang – Pharmacological Research

Animal Models / Animal Microbiome

Holdemanella biformis Improves Glucose Tolerance And Regulates GLP-1 Signaling In obese mice –  Marina Romaní-Pérez – The FASEB Journal

Gut Microbiota Composition Affects Procyanidin A2-Attenuated Atherosclerosis In ApoE(-/-) Mice by Modulating the Bioavailability of Its Microbial Metabolites – Shiying Yang – Journal Of Agricultural And Food Chemistry

The Gut Microbiome Of The Sunda Pangolin (Manis javanica) Reveals Its Adaptation To specialized myrmecophagy – Fuhua Zhang – PeerJ

A Rise In Proteobacteria Is An Indicator Of Gut-liver Axis-mediated Nonalcoholic fatty liver disease in high-fructose-fed adult mice. Isabela Macedo Lopes Vasques-Monteiro – Nutrition Research

Plant Microbiome

Extension Of Plant Phenotypes By The Foliar Microbiome – Christine V Hawkes – Annual Review Of Plant Biology

Plant Genetics As A Tool For Manipulating Crop Microbiomes: Opportunities And Challenges – Kayla M Clouse – Frontiers In Bioengineering And Biotechnology

Development Of An Inexpensive Matrix-assisted Laser Desorption-time Of Flight Mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize – Michael G LaMontagne – PeerJ

Opinion: Assessing The Potential To Harness The Microbiome Through Plant Genetics – Joy Bergelson – Current Opinion In Biotechnology

Experimental and Computational Tools and Techniques

An Integrated Gene Catalog And Over 10,000 Metagenome-assembled Genomes From The gastrointestinal microbiome of ruminants – Fei Xie – Microbiome (BMC)

Antibiotic Resistance: Time Of Synthesis In A Post-genomic Age – Teresa Gil-Gil – Computational And Structural Biotechnology Journal

Efam: An Expanded, Metaproteome-supported HMM Profile Database Of Viral Protein families – Ahmed A Zayed – Bioinformatics

The Future Of Microbial Ecological Niche Theory And Modeling – Stephanie N Kivlin – The New Phytologist

DNA Extraction And Host Depletion Methods Significantly Impact And Potentially Bias Bacterial Detection in a Biological Fluid – Erika Ganda – mSystems

Extremophiles

Electrical Conductivity As A Driver Of Biological And Geological Spatial heterogeneity in the Puquios, Salar de Llamara, Atacama Desert, Chile –  R P Reid – Scientific Reports

June 12, 2021

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Have a nice weekend! Today, in this Digest we have several studies covering different aspects of respiratory tract microbiome, in addition with reproductive tract microbiota. We have also a set of papers covering connections between microbiome, food and diet, as well as some articles about beneficial microbes (a.k.a. probiotics). Take a look also to the papers related with Techniques, Animal and Plant microbiome topics.    

General and Human Microbiome

Review: Ankylosing Spondylitis: An Autoimmune Or Autoinflammatory Disease? – Daniele Mauro – Nature Reviews. Rheumatology

Review: Updated Treatment For Acne: Targeted Therapy Based On Pathogenesis – Ichiro Kurokawa – Dermatology And Therapy

Review: Impact Of Intrapartum Antibiotic Prophylaxis For Group B Streptococcus On The Term Infant Gut Microbiome: A State of the Science Review – Vanessa R Garcia – Journal Of Midwifery & Women’s Health

Review: Cellular And Molecular Mediators Of Lymphangiogenesis In Inflammatory Bowel Disease – Dickson Kofi Wiredu Ocansey – Journal Of Translational Medicine

News in Brief – Microbiome Test Spots Oral Cancers – Nature Biotechnology

Disruption Of The Pro-inflammatory, Anti-inflammatory Cytokines And Tight Junction proteins expression, associated with changes of the composition of the gut  microbiota in patients with irritable bowel syndrome – V Ivashkin – PloS One

The Effect Of The Combined Use Of Silver Diamine Fluoride And Potassium Iodide In disrupting the plaque biofilm microbiome and alleviating tooth discoloration: A  systematic review – Anahita Haiat – PloS One

SARS-CoV-2 Detection Status Associates With Bacterial Community Composition In patients and the hospital environment – Clarisse Marotz – Microbiome

Assessing The Involvement Of The Placental Microbiome And Virome In Preeclampsia using non coding RNA sequencing – Liron Yoffe – Journal Of Perinatal Medicine

An Emerging Role Of Prevotella Histicola On Estrogen Deficiency-induced Bone Loss through the gut microbiota-bone axis in postmenopausal women and in ovariectomized mice – Zhongxiang Wang – The American Journal Of Clinical Nutrition

Supplier-origin Mouse Microbiomes Significantly Influence Locomotor And anxiety-related behavior, body morphology, and metabolism – Aaron C Ericsson – Communications Biology

Microbial Interaction: Prevotella Spp. Reduce P. Aeruginosa Induced Inflammation In cystic fibrosis bronchial epithelial cells –  Anne Bertelsen- Journal Of Cystic Fibrosis

Extra-skeletal Effects Of Dietary Calcium: Impact On The Cardiovascular System, obesity, and cancer – Denise K Daley – Advances In Food And Nutrition Research

The Association Between Bacteria Colonizing The Upper Respiratory Tract And Lower respiratory tract infection in young children: a systematic review and meta-analysis – Shantelle Claassen-Weitz – Clinical Microbiology And Infection

Exploring The Microbiota-Alzheimer’s Disease Linkage Using Short-term Antibiotic treatment followed by fecal microbiota transplantation – Min Wang – Brain, Behavior, And Immunity

Dispersal Strategies Shape Persistence And Evolution Of Human Gut Bacteria – Falk Hildebrand – Cell Host & Microbe

Review: The Impact Of The Female Genital Tract Microbiome In Women Health And Reproduction: a review – Paula Punzón-Jiménez – Journal Of Assisted Reproduction And Genetics

Dysosmobacter Welbionis Is A Newly Isolated Human Commensal Bacterium Preventing diet-induced obesity and metabolic disorders in mice – Tiphaine Le Roy – Gut (BMJ)

Citizen-science Based Study Of The Oral Microbiome In Cystic Fibrosis And Matched controls reveals major differences in diversity and abundance of bacterial and  fungal species – Jesse R Willis – Journal Of Oral Microbiology

Microbiome, Food and Diet

Legume Consumption And Gut Microbiome In Elderly Chinese Men And Women – Cong Wang – The Journal Of Nutrition

Gut Health Function Of Instant Dehydrated Rice Sticks Substituted With Resistant Starch Types 2 and 4 – Nisa Alfilasari – Current Microbiology

Microalgae As Feed Ingredients: Recent Developments On Their Role In immunomodulation and gut microbiota of aquaculture species – Uma Shankar Sagaram – FEMS Microbiology Letters

Plant-Based Diet Index And Metabolic Risk In Men: Exploring The Role Of The Gut Microbiome – Yanping Li – The Journal Of Nutrition

Beneficial Microbes and Compounds

The Effects Of Limosilactobacillus Reuteri LR-99 Supplementation On Body Mass Index, Social Communication, Fine Motor Function, and Gut Microbiome Composition in  Individuals with Prader-Willi Syndrome: a Randomized Double-Blinded  Placebo-Controlled Trial – Xue-Jun Kong – Probiotics And Antimicrobial Proteins

Lactobacillus Paracasei Modulates The Gut Microbiota And Improves Inflammation In type 2 diabetic rats – Zhu Zeng – Food & Function

Mixture Of Probiotics Reduces Inflammatory Biomarkers And Improves The oxidative/nitrosative profile in people with rheumatoid arthritis – Ligia Aparecida Trintin Cannarella – Nutrition

Xiao-Chai-Hu-Tang Ameliorates Tumor Growth In Cancer Comorbid Depressive Symptoms via modulating gut microbiota-mediated TLR4/MyD88/NF-kB signaling pathway – Shiyun Shao- Phytomedicine

Lactobacillus Rhamnosus GG Orchestrates An Anti-tumor Immune Response – Joshua A Owens – Cellular And Molecular Gastroenterology And Hepatology

Lactobacillus Strains Derived From Human Gut Ameliorate Metabolic Disorders Via modulation of gut microbiota composition and short-chain fatty acids metabolism – G Wang – Beneficial Microbes

Animal Microbiome

Review: The Specification And Function Of Enteroendocrine Cells In Drosophila And Mammals: A Comparative – Xingting Guo – The FEBS Journal

Enterocins As Novel Feed Additives In Rabbit Diet: Enterocin Ent M And Durancin Ent ED26E/7, Their Combination, and Effects on Microbiota, Caecal Fermentation, and  Enzymatic Activity – M. Pogány Simonová – Probiotics And Antimicrobial Proteins

The Effect Of Lipid Metabolism Regulator Anthocyanins From Aronia Melanocarpa On 3T3-L1 preadipocytes and C57BL/6 mice via activating AMPK signaling and gut microbiota – Chunping Chen – Food & Function

A Probiotic Has Differential Effects On Allergic Airway Inflammation In A/J And C57BL/6 mice and is correlated with the gut microbiome – Mateus B Casaro – Microbiome

16S RRNA Gene Amplicon Sequencing Of Gut Microbiota From Naked Carp (Gymnocypris przewalskii) in Qinghai Lake, China – Fayan Wang – Microbiology Resource Announcements

Sulfated Modification Enhances The Modulatory Effect Of Yam Polysaccharide On Gut microbiota in cyclophosphamide-treated mice –  Rong Huang – Food Research International 

Diversity And Interactions Among Triatomine Bugs, Their Blood Feeding Sources, Gut microbiota and Trypanosoma cruzi in the Sierra Nevada de Santa Marta in Colombia – Claribel Murillo-Solano – Scientific Reports

Rumen Microbiota Of Tibetan Sheep (Ovis Aries) Adaptation To Extremely Cold Season on the Qinghai-Tibetan Plateau – Qingshan Fan – Frontiers In Veterinary Science

Plant Microbiome

Phytohormones Selectively Affect Plant Parasitic Nematodes Associated With Arabidopsis roots.-  Md Maniruzzaman Sikder- The New Phytologist

Bacterial Community Structure And The Dominant Species In Imported Pollens For Artificial Pollination –  Su-Hyeon Kim – The Plant Pathology Journal

Structure And Variation Of Root-associated Bacterial Communities Of Cyperus Rotundus L. in the contaminated soils around Pb/Zn mine sites – Pin Gao – Environmental Science And Pollution Research International

Antibiotic Resistance Gene-Carrying Plasmid Spreads Into The Plant Endophytic Bacteria using Soil Bacteria as Carriers – Han Xu – Environmental Science & Technology

Flavonoids And Saponins In Plant Rhizospheres: Roles, Dynamics, And The Potential for agriculture – Akifumi Sugiyama – Bioscience, Biotechnology, And Biochemistry

Host Specific Endophytic Microbiome Diversity And Associated Functions In Three varieties of scented black rice are dependent on growth stage – K Malabika Singha- Scientific Reports

Microbiome: Bioinformatics and Techniques

Constraining PERMANOVA And LDM To Within-set Comparisons By Projection Improves The efficiency of analyses of matched sets of microbiome data – Zhengyi Zhu – Microbiome

Interrogating The Bovine Reproductive Tract Metagenomes Using Culture-independent approaches: a systematic review – Chian Teng Ong – Animal Microbiome

Laboratory Aspects Of Donor Screening For Fecal Microbiota Transplantation At A Korean Fecal Microbiota Bank –  Hyun Soo Seo – Annals Of Laboratory Medicine

Profiling System Of Oral Microbiota Utilizing Polymerase Chain Reaction-restriction fragment length polymorphism analysis – Hiroto Sano – Journal Of Oral Biosciences

Review: Organoids And Organs-on-chips: Insights Into Human Gut-microbe Interactions – Jens Puschhof – Cell Host & Microbe

Development Of A Time-series Shotgun Metagenomics Database For Monitoring Microbial communities at the Pacific coast of Japan –  Kazutoshi Yoshitake – Scientific Reports

Other

Silicon Dioxide Nanoparticles Induced Neurobehavioral Impairments By Disrupting microbiota-gut-brain axis – Jun Diao – Journal Of Nanobiotechnology

Decay Of Infectious SARS-CoV-2 And Surrogates In Aquatic Environments – Laura Sala-Comorera –  Water Research

The Efficacy And Effect On Gut Microbiota Of An Aflatoxin Binder And A Fumonisin esterase using an in vitro simulator of the human intestinal microbial ecosystem  (SHIME®) – Kaat Neckermann – Food Research International

June 8, 2021

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Human gut microbiome

Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome – Bolte et al. Gut

Ginseng polysaccharides alter the gut microbiota and kynurenine/tryptophan ratio, potentiating the antitumour effect of antiprogrammed cell death 1/programmed cell death ligand 1 (anti-PD-1/PD-L1) immunotherapy – Huang et al. Gut

Human skin microbiome

Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching – Wilkins et al. Microbiome.

Animal microbiome

Host Species and Geography Differentiate Honeybee Gut Bacterial Communities by Changing the Relative Contribution of Community Assembly Processes – Ge et al. mBio

Animal experiments

Dysbiosis exacerbates colitis by promoting ubiquitination and accumulation of the innate immune adaptor STING in myeloid cells – Shmuel-Galia et al. Immunity

Water Microbiome

Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir – Mo et al. Microbiome

Phages and viruses

A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases – Tisza and Buck. PNAS. 

Bioinformatics

A Critique of Differential Abundance Analysis, and Advocacy for an Alternative – Quinn et al. arXiv preprint. 

June 4, 2021

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Greetings from Pittsburgh!

Today’s digest includes a review about the digestibility of adult dog diets, several articles about the human gut microbiome, an article about the spinach phyllosphere, and research about the effect of fertilizer and continuous garlic cultivation on the soil microbiome. It also includes topics such as microorganisms in ancient Siberian permafrost, the use of a probiotic consortium as an alternative to chemical remediation of oil spills, and much more!

If you want a lighter read, I’ve also included a fun Smithsonian Magazine article about the use of bacteria in art restoration.

Happy Friday!

General microbiome

Review: An evolving view on biogeochemical cycling of iron – Kappler et al. – Nature Reviews Microbiology

Review: Beyond horizontal gene transfer: the role of plasmids in bacterial evolution – Rodríguez-Beltrán et al. – Nature Reviews Microbiology

Review: Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle – Salje – Nature Reviews Microbiology

Reviews: Microbial volatile organic compounds in intra-kingdom and inter-kingdom interactions – Weisskopf et al. – Nature Reviews Microbiology

Human skin microbiome

Apple cider vinegar soaks do not alter the skin bacterial microbiome in atopic dermatitis – Luu et al. – PLOS One

Human gut microbiome

Metabolomic profiling identifies complex lipid species and amino acid analogues associated with response to weight loss interventions – Bihlmeyer et al. – PLOS One

Gut microbiome differences among Mexican Americans with and without type 2 diabetes mellitus – Kitten et al. – PLOS One

Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank – Liu et al. – Microbiome

Gut microbiota profiles of young South Indian children: Child sex-specific relations with growth – Shivakumar et al. – PLOS One

Animal experiments

Review: Soybean meal and poultry offal meal effects on digestibility of adult dogs diets – Vanelli et al. – PLOS One

Animal microbiome

A survey of mosquito-borne and insect-specific viruses in hospitals and livestock markets in western Kenya – Chiuya et al. – PLOS One

Microbiomes of clownfish and their symbiotic host anemone converge before their first physical contact – Émie et al. – Microbiome

Characterization of oral and cloacal microbial communities in cold-stunned Kemp’s ridley sea turtles (Lepidochelys kempii) during the time course of rehabilitation – McNally et al. – PLOS One

Plant, root, and soil microbiome

Influence of seasonal changes and salinity on spinach phyllosphere bacterial functional assemblage – Ibekwe et al. – PLOS One

Comparison of bacterial and archaeal communities in two fertilizer doses and soil compartments under continuous cultivation system of garlic – Zhou et al. – PLOS One

Water and extremophile microbiome

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale – Carnevali et al. – Microbiome

Urban wastewater bacterial communities assemble into seasonal steady states – LaMartina et al. – Microbiome

Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost – Liang et al. – Microbiome

Genomic and immunogenic changes of Piscine novirhabdovirus (Viral Hemorrhagic Septicemia Virus) over its evolutionary history in the Laurentian Great Lakes – Niner et al. – PLOS One

Built environment

Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites – Silva et al. – Microbiome

Microbes in the news

Italian Art Restorers Used Bacteria to Clean Michelangelo Masterpieces – Davis-Marks – Smithsonian Magazine

May 29, 2021

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General microbiome

Biogeochemical dynamics and microbial community development under sulfate- and iron-reducing conditions based on electron shuttle amendment – TM Flynn et al. – PLOS ONE

Human skin microbiome

Composition of cutaneous bacterial microbiome in seborrheic dermatitis patients: A cross-sectional study – MGH Sanders et al. – PLOS ONE

Human gut microbiome

Host specificity of the gut microbiome – EK Mallot & KR Amato – Nature Reviews Microbiology

Animal experiments

Influence of genetic background and dietary oleic acid on gut microbiota composition in Duroc and Iberian pigs – A López-Garcí et al. – PLOS ONE

Animal microbiome

Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees – M Callegari et al. – npj Biofilms and Microbiomes

Plant, root, and soil microbiome

Saprotrophic fungal diversity predicts ectomycorrhizal fungal diversity along the timberline in the framework of island biogeography theory – T Yang et al. – ISME Communications

Soil microbial community responses to short-term nitrogen addition in China’s Horqin Sandy Land – N Yayi et al. – PLOS ONE

Specificity of assemblage, not fungal partner species, explains mycorrhizal partnerships of mycoheterotrophic Burmannia plants – Z Zhao et al. – The ISME Journal

Water and extremophile microbiome

Abundant and rare bacterial taxa structuring differently in sediment and water in thermokarst lakes in the Yellow River Source area, Qinghai-Tibet Plateau – Z Ren et al. – bioRxiv

Phages and viruses

Diversity, taxonomy and evolution of archaeal viruses of the class Caudoviricetes – Y Liu et al. – bioRxiv

Integrating Viral Metagenomics into an Ecological Framework – P Sommers et al. – Annual Review of Virology

Techniques

Spatial profiling of microbial communities by sequential FISH with error-robust encoding – Z Cao et al. – bioRxiv

May 28, 2021

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Good morning from New Jersey! A broad selection of papers to share with you today—highlights include several new bioinformatics papers and an examination of the effect of storage method on the composition of microbiome samples:

General microbiome

A global metagenomic map of urban microbiomes and antimicrobial resistance, David Danko et al., Cell

Ecology and molecular targets of hypermutation in the global microbiome, Simon Roux et al., Nature Communications

Human oral microbiome

A cocoa (Theobroma cacao L.) extract impairs the growth, virulence properties, and inflammatory potential of Fusobacterium nucleatum and improves oral epithelial barrier function, Amel Ben Lagha et al., PLOS ONE

Human skin microbiome

Composition of cutaneous bacterial microbiome in seborrheic dermatitis patients: A cross-sectional study, Martijn G.H. Sanders et al., PLOS ONE

Human gut microbiome

Gene-level metagenomic architectures across diseases yield high-resolution microbiome diagnostic indicators, Braden T. Tierney et al., Nature Communications

Altered faecal microbiome and metabolome in IgG4-related sclerosing cholangitis and primary sclerosing cholangitis, Qiaoyan Liu et al., Gut

Animal experiments

Gut microbiome variation modulates the effects of dietary fiber on host metabolism, Sofia M. Murga-Garrido et al., Microbiome

Real-time monitoring of ruminal microbiota reveals their roles in dairy goats during subacute ruminal acidosis, Xiaodong Chen et al., npj Biofilms and Microbiomes

Animal microbiome

The microbiome and mosquito vectorial capacity: rich potential for discovery and translation, Cintia Cansado-Utrilla et al., Microbiome

Bioinformatics

Preprint: A metabolomics pipeline enables mechanistic interrogation of the gut microbiome, Shuo Han et al., bioRxiv

Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing, Zachary D. Wallen, BMC Bioinformatics

Reads Binning Improves the Assembly of Viral Genome Sequences From Metagenomic Samples, Kai Song, Frontiers in Microbiology

Techniques

Preprint: Standard Sample Storage Conditions Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns, Casper Sahl Poulsen et al., bioRxiv

May 22, 2021

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Have a good weekend! Today in this Digest, we have several papers, including reviews about microbiome and obesity or cancer, microbiome restoration, new research with new Akkermansia isolates, and a meta-analysis showing the effect of synbiotics on ulcerative colitis. We have as well several studies in different animal models (from primates to C. elegans). We also highlight some papers on different technical aspects of microbiome analysis, including a multi-center study assessing the impact of bioinformatic procedures in microbiome analysis.   

Human and General Microbiome

Review: The Influence of Gut Microbiota on the Cardiovascular System Under Conditions of Obesity and Chronic Stress – Piotr Dubinski – Current Hypertension Reports 

Review: Restoration of dysbiotic human gut microbiome for homeostasis – Kunal Dixit – Life Sciences 

Review: The role of microbiome in colorectal carcinogenesis and its clinical potential as a target for cancer treatment –  Sang Hoon Kim – Intestinal Research 

Meta-analysis: Synbiotics improve clinical indicators of ulcerative colitis: systematic review with meta-analysis– Marcos Natal Rufino – Nutrition reviews 

Metformin Affects Gut Microbiome Composition and Function and Circulating Short-Chain Fatty Acids: A Randomized Trial – Noel T Mueller – Diabetes Care 

Genotypic and Phenotypic Diversity among Human Isolates of Akkermansia muciniphila – Bradford Becken – mBio 

Association of Gut Microbiota during Early Pregnancy with Risk of Incident Gestational Diabetes Mellitus – Ping Hu – The Journal of clinical endocrinology and metabolism 

Maternal precarity and HPA axis functioning shape infant gut microbiota and HPA axis development in humans – Johanna R Jahnke – PLoS ONE

Profiling of tumour-associated microbiota in human hepatocellular carcinoma – Seiga Komiyama – Scientific Reports 

Perceived Stress and Molecular-BV in the NIH Longitudinal Study of Vaginal Flora – Rodman Turpin- American Journal of Epidemiology 

Genetically Programmable Microbial Assembly – Mark T Kozlowski – ACS Synthetic Biology 

Regulatory role of the intestinal microbiota in the immune response against Giardia – B Maertens – Scientific Reports 

Role of microbiota-gut-brain axis dysfunctions induced by infections in the onset of anorexia nervosa– Marie Galmiche – Nutrition Reviews 

Blood microbiota and metabolomic signature of major depression before and after antidepressant treatment: a prospective case-control study – Dragos Ciocan – Journal of Psychiatry & Neuroscience

Combined analysis of metagenomic data revealed consistent changes of gut microbiome structure and function in inflammatory bowel disease – Yangliu Xia – Journal of Applied Microbiology 

Stability of the human gut virome and effect of gluten-free diet – Sanzhima Garmaeva – Cell Reports 

Animal Microbiome

Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria – Christian Zenner – mSystems 

Extinction of anciently associated gut bacterial symbionts in a clade of stingless bees – Alan Emanuel Silva Cerqueira –  The ISME Journal 

Utilizing the Microbiota and Machine Learning Algorithms to Assess Risk of Salmonella Contamination in Poultry Rinsate – Hannah Bolinger – Journal of Food Protection 

Influence of genetic background and dietary oleic acid on gut microbiota composition in Duroc and Iberian pigs – Adrián López-García – PLoS ONE

Predictable and host-species specific humanization of the gut microbiota in captive primates – Jennifer L Houtz  – Molecular Ecology 

The symbiotic relationship between Caenorhabditis elegans and members of its microbiome contributes to worm fitness and lifespan extension – Orçun Haçariz – BMC Genomics 

Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients – Remi N Ketchum – Molecular Ecology 

Live and ultrasound-inactivated Lacticaseibacillus casei modulate the intestinal microbiota and improve biochemical and cardiovascular parameters in male rats fed a high-fat diet – Larissa Ramalho Brandão – Food & Function 

Glycan-based shaping of the microbiota during primate evolution – Sumnima Singh – eLife 

Regulatory effect of non-starch polysaccharides from purple sweet potato on intestinal microbiota of mice with antibiotic-associated diarrhea – Nana Bie – Food & Function 

Regulatory effect of volatile compounds in fermented alcoholic beverages on gut microbiota and serum metabolism in a mouse model – Mei Ji – Food & Function 

Plant Microbiome

Targeted 16S rRNA gene and ITS2 amplicon sequencing of leaf and spike tissues of Piper longum identifies new candidates for bioprospecting of bioactive compounds – Sushma Mishra – Archives of Microbiology 

Absence of Nanoparticle-Induced Drought Tolerance in Nutrient Sufficient Wheat Seedlings – Matthew Potter – Environmental Science & Technology 

Extremophiles

Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil – Yunha Hwang – mSystems 

Techniques

Review: Identifying biases and their potential solutions in human microbiome studies – Jacob T Nearing – Microbiome 

Commentary: Application of Machine Learning in Translational Medicine: Current Status and Future Opportunities – Nadia Terranova – The AAPS Journal 

An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities – Denise M O’Sullivan – Scientific Reports 

A semiparametric model for between-subject attributes: Applications to beta-diversity of microbiome data – J Liu – Biometrics 

Other

The potential and effects of saline-alkali alfalfa microbiota under salt stress on the fermentation quality and microbial – Duo Wen Sa – BMC Microbiology 

May 17, 2021

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Good morning from Pittsburgh.

Today’s digest is preprint-heavy and has quite a few articles focused on soil, plants, and agriculture. If you aren’t interested in those areas of research, we also have articles with topics spanning the 1918 pandemic to multi-donor fecal transplants to carbohydrate utilization by marine fungi.

Happy reading!

General microbiome

Fresh extension of Vibrio cholerae competence type IV pili predisposes them for motor-independent retraction – Chlebek et al. – Appl Environ Microbiol

Preprint: Coordination of gene expression with cell size enables Escherichia coli to efficiently maintain motility across conditions – Honda et al. – bioRxiv

Preprint: Archival influenza virus genomes from Europe reveal genomic and phenotypic variability during the 1918 pandemic – Patrono et al. – bioRxiv

Preprint: Fluorescent protein expression as a proxy of bacterial fitness in a high throughput assay – Schlechter et al. – bioRxiv

Preprint: Nanopore sequencing provides rapid and reliable insight into microbial profiles of Intensive Care Units – Viana de Siqueira et al. – bioRxiv

Human skin microbiome

Preprint: Anatomy promotes neutral coexistence of strains in the human skin microbiome – Conwill et al. – bioRxiv

Preprint: Gene- and genome-centric dynamics shape the diversity of oral bacterial populations – Utter et al. – bioRxiv

Human gut microbiome

Preprint: Two microbiota subtypes identified in Irritable Bowel Syndrome with distinct responses to the low-FODMAP diet – Vervier et al. – bioRxiv

Strain engraftment competition and functional augmentation in a multi-donor fecal microbiota transplantation trial for obesity – Wilson et al. – Microbiome

Plant, root, and soil microbiome

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula – Brown et al. – Microbiome

Preprint: A novel dual enrichment strategy provides soil- and digestate-competent N2O-respiring bacteria for mitigating climate forcing in agriculture – Jonassen et al. – bioRxiv

Preprint: Temporal dynamics of microbial transcription in wetted hyperarid desert soils – León-Sobrino et al. – bioRxiv

Preprint: Metagenomic sequencing for rapid identification of Xylella fastidiosa from leaf samples – Roman-reyna et al. – BioRxiv

Preprint: Pseudomonas arenae sp. nov., Pseudomonas glycinis sp. nov. and Pseudomonas harudinis sp. nov., three novel bacterial species and plant endophytes – Seaton et al. – bioRxiv

Preprint: Phage-resistant bacteria reveal a role for potassium in root colonization – Tzipilevich & Benfey – bioRxiv

Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems – Qian et al. – Microbiome

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

Potential and expression of carbohydrate utilization by marine fungi in the global ocean – Baltar et al. – Microbiome

Preprint: Syntrophic H2 production enhances the performance of primarily acetate-supplemented reactors treating sulphate contaminated solutions – Hessler et al. – bioRxiv

May 14, 2021

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Today’s digest features Emu for microbial community profiling with expectation-maximization algorithm to generate taxonomic abundance profiles from full-length 16S rRNA reads, glycobiology of UTI, profiling canine fecal microbiome by long-read metagenomics with Nanopore sequencing, spatial-temporal assessment of drinking water microbiome in Puerto Rico, ancient microbial genomes from paleofeces (with 61 previously undescribed species), and more.

Check out a list of awesome webinars, courses and podcasts. Happy Friday!

Today is the last day for #NSURP2021 applications:

The National Summer Undergraduate Research Project – A community-driven initiative to create rewarding remote summer research opportunities for BIPOC and Latinx undergraduate students in the microbial sciences.

Share your experience as an early career researcher with your academic mentor and take part in this important survey on mentorship!

Gut microbiome

Reconstruction of ancient microbial genomes from the human gut – Marsha C. Wibowo – Nature

Human and preclinical studies of the host–gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health – François Brial – Gut Microbiota

Oral microbiome

*Mechanical biofilm disruption causes microbial and immunological shifts in periodontitis patients – William Johnston – Scientific Reports

Vaginal microbiome

Review: The Complex Link between the Female Genital Microbiota, Genital Infections, and Inflammation – Smritee Dabee – Infection and Immunity

Urinary microbiome

*Review: The glycobiology of uropathogenic E. coli infection: the sweet and bitter role of sugars in urinary tract immunity – Federico Lupo – Immunology

The Good and the Bad: Ecological Interaction Measurements Between the Urinary Microbiota and Uropathogens – Laurens E. Zandbergen – Frontiers in Microbiology

Urinary prostaglandin E2 as a biomarker for recurrent UTI in postmenopausal women – Tahmineh Ebrahimzadeh – Life Science Alliance

Impact of Vaginal Estrogen on the Urobiome in Postmenopausal Women With Recurrent Urinary Tract Infection – Carrie E. Jung – Female Pelvic Medicine & Reconstructive Surgery

Animal microbiome

*Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces – Anna Cuscó – BMC Genomics

Perinatal exposure to tetracycline contributes to lasting developmental effects on offspring – Elizabeth M. Hill – Animal Microbiome

Drinking water microbiome

*Spatial-temporal targeted and non-targeted surveys to assess microbiological composition of drinking water in Puerto Rico following Hurricane Maria – Maria Catalina Sevillano – bioRxiv

Technique

Predicting the presence and abundance of bacterial taxa in environmental communities through flow cytometric fingerprinting – Jasmine Heyse – bioRixv

Sample preservation

Critical evaluation of faecal microbiome preservation using metagenomic analysis – Alena L. Pribyl – ISME Communications

Bioinformatics

*Emu: Species-Level Microbial Community Profiling for Full-Length Nanopore 16S Reads – Kristen D. Curry – bioRxiv

Microbiome differential abundance methods produce disturbingly different results across 38 datasets – Jacob T Nearing – bioRxiv

Improving metagenomic binning results with overlapped bins using assembly graphs – Vijini G. Mallawaarachchi – Algorithms for Molecular Biology

A method for achieving complete microbial genomes and improving bins from metagenomics data – Lauren M. Lui – Plos Computational Biology

Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions – J. Lima – Journal of Microbiological Methods

Webinars

EMBARK Spring Webinars – Heike Schmitt “International efforts for One Health surveillance of AMR (WHO Tricycle)” and Etienne Ruppé “On the use of Tricycle in EMBARK” – EMBARK project – May 19
Registration here
More info here

BISMiS Live – GCM 2.0: WDCM 10K Sequencing Project for Type Strains by Juncai Ma – Bergey’s Intl. Society for Microbial Systematics – May 15
Registration here
More info here

Women in Data Science 2021 – Perspectives in Industry and Academia – Bayer AG and de.NBI, Elixir Germany Event – 18 June

PPGSND thesis seminar: The dark side os science: misconduct in biomedical research – Elisabeth Bik – 20 May

mSystems Thinking Series – ASM

Courses

Riffomonas Project – R tutorials and more – PatricK Schloss

Machine learning in Python with scikit-learn – Inria

Introduction to Computer Science and Programming in Python – MIT

Using MOFA for integration of omics data – Ricard Argelaguet – May 25

Data Visualization: Use R, ggplot2, and the principles of graphic design to create beautiful and truthful visualizations of data – Andrew Heiss

Conferences

1st Young AMICI Symposium – Austrian Microbiome Initiative – May 25-26

Microbes, Social Equity, and Rural Health – The Microbes and Social Equity working group and The University of Maine Institute of Medicine – June 14–18

Podcast

Differential gene expression and DESeq2 with Michael Love – The Bioinformatics Chat – Roman Cheplyaka and Jacob Schreiber

The Fake Science Detectives with David Sanders and Elisabeth Bik – Follow the Science – Faye Flam

Research, networking and public perception of science with Linda J Kenney – Microbes and Us – Joseph Shuttleworth

The microbiome: Delicious food and solutions to the climate crisis with Lene Lange – Science Stories – Jens Degett