July 6, 2021

Several great papers today including a very interesting Cell paper on how Bifidobacterium interacts with the immune system and an mBio article on how different types of dietary fibre shape the gut microbiota.

To our Australian readers I’d like to wish a happy NAIDOC week, which is a time to celebrate the history, culture and achievements of Aboriginal and Torres Strait Islander peoples.

General microbiome

Microbiota regulate social behaviour via stress response neurons in the brain – Wu et al. Nature. 

Defining the resilience of the human salivary microbiota by a 520-day longitudinal study in a confined environment: the Mars500 mission – Bacci et al. Microbiome

A MicroRNA Gene Panel Predicts the Vaginal Microbiota Composition. Cheng et al. mSystems

Human gut microbiome

Gut microbiota mediate the FGF21 adaptive stress response to chronic dietary protein-restriction in mice – Martin et al. Nature Communications. 

Gut microbes impact stroke severity via the trimethylamine N-oxide pathway – Zhu et al. Cell Host & Microbe

Dietary Fiber Hierarchical Specificity: the Missing Link for Predictable and Strong Shifts in Gut Bacterial Communities – Centu-Jungles et al. mBio

Pregnancy and Early-Life

Bifidobacteria-mediated immune system imprinting early in life – Henrick et al. Cell

Animal microbiome

Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions – Lejal et al. Microbiome

Water Microbiome

Microbiome diversity and host immune functions influence survivorship of sponge holobionts under future ocean conditions – Posadas et al. ISME

Soil microbiome

A Community Effort: Combining Functional Amplicon Sequencing and Metagenomics Reveals Potential Biosynthetic Gene Clusters Associated with Protective Phenotypes in Rhizosphere Microbiomes – Winter. mSystems.

Bioinformatics

METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses – Milani et al. mSystems

July 4, 2021

Have a nice Sunday! (and a happy July 4th to Americans!) In this digest, we have a set of papers covering different areas of microbiome research, including 3 studies covering aspects of the relationship between COVID19 and microbiome, pan-genomic, and metatranscriptomic studies from probiotic microbes, and the role of the aryl hydrocarbon receptor in the host-microbiome communication.   

Human and General Microbiome

Review: The Relationship Between The Gut Microbiome And Neurodegenerative Diseases – Xueling Zhu – Neuroscience Bulletin

Systematic Review: Exploring The Role Of Respiratory Microbiome In Lung Cancer: A Systematic Review – Fabiana Perrone – Critical Reviews In Oncology/Hematology

Commensal Microbiota Regulates Skin Barrier Function And Repair Via Signaling through the aryl hydrocarbon receptor – Aayushi Uberoi – Cell Host & Microbe

Tryptophan-metabolizing Gut Microbes Regulate Adult Neurogenesis Via The Aryl hydrocarbon receptor – George Zhang Wei – Proceedings Of The National Academy Of Sciences Of The United States Of America

Mucosa-associated Gut Microbiota Reflects Clinical Course Of Ulcerative Colitis – Yuichiro Nishihara – Scientific Reports

Helicobacter pylori Infection-induced Changes In The Intestinal Microbiota Of 14-year-old or 15-year-old Japanese adolescents: a cross-sectional study – Toshihiko Kakiuchi – BMJ Open

The Infant Gut Resistome Is Associated With E. coli And Early-life Exposures – Rebecca M Lebeaux – BMC Microbiology

The Gut Microbiome Of Heart Failure With Preserved Ejection Fraction – Anna L Beale – Journal Of The American Heart Association

Association Of Gut Microbiomes With Lung And Esophageal Cancer: A Pilot Study – Weitao Shen – World Journal Of Microbiology & Biotechnology

Vaginal Lactobacilli And Vaginal Dysbiosis-Associated Bacteria Differently Affect Cervical Epithelial and Immune Homeostasis and Anti-Viral Defenses – Sabrina Nicolò – International Journal Of Molecular Sciences

Finding A Balance In The Vaginal Microbiome: How Do We Treat And Prevent The Occurrence of Bacterial Vaginosis? – Rebecca Jane Joseph – Antibiotics (MDPI)

Mycobiome And Cancer: What Is The Evidence? – Natalia Vallianou – Cancers

Characterizing The Effects Of Calcium And Prebiotic Fiber On Human Gut Microbiota Composition and Function Using a Randomized Crossover Design-A Feasibility Study – Lara S Yoon – Nutrients

Gut Microbiota Profile And Its Association With Clinical Variables And Dietary Intake in Overweight/Obese and Lean Subjects: A Cross-Sectional Study – Judit Companys – Nutrients

Microbiome and COVID19

Review: Modulation Of Gut Microbiota For The Prevention And Treatment Of COVID-19 – Jiezhong Chen – Journal Of Clinical Medicine

COVID-19 Lockdowns May Reduce Resistance Genes Diversity In The Human Microbiome And the Need for Antibiotics – João S Rebelo – International Journal Of Molecular Sciences

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

Beneficial Microbes and Compounds

Flavonoids From Whole-Grain Oat Alleviated High-Fat Diet-Induced Hyperlipidemia Via Regulating Bile Acid Metabolism and Gut Microbiota in Mice – Ruiqian Duan – Journal Of Agricultural And Food Chemistry

Novel Targeted Biological Agents For The Treatment Of Atopic Dermatitis – Nan Yang – BioDrugs 

Escherichia coli Nissle 1917 As Adjuvant Therapy In Patients With Chronic Bacterial prostatitis: a non-blinded, randomized, controlled trial – Celeste Manfredi – World Journal Of Urology

Influence Of Lactobacillus Paracasei HII01 Supplementation On Glycemia And Inflammatory Biomarkers in Type 2 Diabetes: A Randomized Clinical Trial – Parichart Toejing – Foods (MDPI) 

Dietary Habits And Gut Microbiota In Healthy Adults: Focusing On The Right Diet. A Systematic Review – Giulia Gibiino – International Journal Of Molecular Sciences

Animal Microbiome

Review: Potential Of Bacillus velezensis As A Probiotic In Animal Feed: A Review – Fatima Khalid – Journal Of Microbiology

Metagenomics Analysis Revealed The Distinctive Ruminal Microbiome And Resistive profiles in dairy buffaloes – Hui-Zeng Sun – Animal Microbiome

Composition And Diversity Of Gut Microbiota In Pomacea canaliculata In Sexes And between developmental stages – Lian Chen – BMC Microbiology

Plant and Soil Microbiome

Microbiome-mediated Effects Of Habitat Fragmentation On Native Plant Performance – Kasey N Kiesewetter – The New Phytologist

Improvement Of Soil Microbial Diversity Through Sustainable Agricultural Practices and Its Evaluation by -Omics Approaches: A Perspective for the Environment, Food  Quality and Human Safety – Marta Bertola – Microorganisms (MDPI)

Leaf Metabolic Influence Of Glyphosate And Nanotubes On The Arabidopsis Thaliana phyllosphere – Mingjing Ke – Journal Of Environmental Sciences

Bioinformatics and Genomics

Comprehensive Pan-Genome Analysis Of Lactiplantibacillus plantarum Complete Genomes– Francesco M Carpi – Journal Of Applied Microbiology

Metagenomic And Metatranscriptomic Profiling Of Lactobacillus casei Zhang In The Human Gut – Jicheng Wang – NPJ Biofilms And Microbiomes

PhyLoSTM: A Novel Deep Learning Model On Disease Prediction From Longitudinal microbiome data – Divya Sharma – Bioinformatics

Joint Modeling Of Zero-inflated Longitudinal Proportions And Time-to-event Data With application to a gut microbiome study. – Jiyuan Hu – Biometrics

July 2nd, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a selection of interesting gut microbiome papers and preprints. In particular, Beller et al. looked at the succession of microbial communities in the infant gut from birth to 1 year of age. This digest also contains some very interesting works on environmental microbiome, as an example, Wasmund et al. investigated bacterial taxa able to degrade extracellular DNA in marine sediments.

For those interesting in bioinformatic tools and methods, this digest also contains the description of novel data ressources and tools. In particular, Pellow et al. present a new tool, SCAPP, allowing for a better assembly of plasmids from metagenomes.

Finally, today’s non-microbiology pick is a paper looking critically at the open source citation advantage effect (the hypothesis that articles made available open access may benefit from an increased number of citation) by conducting a meta-analysis of previous studies.

Have a great Weekend!


Multi-site human microbiome

Review: The human microbiome and COVID-19: A systematic review – Yamamoto et al. – Plos One

Human gut microbiome

The gut microbiome and type 2 diabetes status in the Multiethnic Cohort – Maskarinec et al. – Plos One

Preprint: Niche partitioning facilitates coexistence of closely related gut bacteria – Brochet et al. – BiorXiV

Preprint: Successional Stages in Infant Gut Microbiota Maturation – Beller et al. – BiorXiV

Fetal meconium does not have a detectable microbiota before birth – Kennedy et al. – Nature Microbiology


Animal experiments

Developmental intestinal microbiome alterations in canine fading puppy syndrome: a prospective observational study – Tal et al. – NPJ Biofilms and Microbiomes

Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance – Liu et al. – Nature Microbiology

Animal microbiome

Preprint: Enteric viruses nucleic acids distribution along the digestive tract of rhesus macaques with idiopathic chronic diarrhea – Delwart et al. – BiorXiV

Plant, root, and soil microbiome

Microbiomes of commercially-available pine nuts and sesame seeds – Fay et al. – Plos One

Spatial patterns in phage-Rhizobium coevolutionary interactions across regions of common bean domestication – Van Cauwenberghe et al. – ISME Journal

Water and extremophile microbiome

Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments – Wasmund et al. – Nature Microbiology


Phages and viruses

Preprint: High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems – Meaden et al. – BioRxiV

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome – Nayfach et al. – Nature Microbiology

Bioinformatics

SCAPP: an algorithm for improved plasmid assembly in metagenomes – Pellow et al. – Microbiome

A standardized archaeal taxonomy for the Genome Taxonomy Database – Rinke et al. – Nature Microbiology


My non-microbiology picks

Is the open access citation advantage real? A systematic review of the citation of open access and subscription-based articles – Langham-Putrow et al. – Plos One

June 25, 2021

This week, the microbial sciences community worldwide (virtually) united at the World Microbe Forum – meeting highlights you can find here #WorldMicrobeForum.

Today’s digest features studies on group B Streptococcus pathogenesis, dental microbiota and aGVHD Risk, a book about writing and publishing papers, and more. Also, check out a collection of FREE, ONLINE microbiome events. Happy Friday!


Read about the experiences of 338 early career researchers from 36 countries with their mentors in Mentorship in life sciences: voices of mentees by A. Murat Eren (Meren)!


General microbiome

Behind the paper: Describing and naming bacteria in the 21st century – Thomas Hitch – Nature blog

Hierarchical control of microbial community assembly – Sammy Pontrelli – bioRxiv

Resistome

*L-form switching confers antibiotic, phage and stress tolerance in pathogenic Escherichia coli – Aleksandra Petrovic Fabijan – bioRxiv

Gut microbiome

A newly identified protein from Akkermansia muciniphila stimulates GLP-1 secretion – Patrice D. Cani and Claude Knauf – Cell Metabolism

Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics – Anna Pryszlak – arXiv

Dispersal strategies shape persistence and evolution of human gut bacteria – Falk Hildebrand – Cell Host & Microbe

Urinary microbiome

Review: Urinary Microbiome: Yin and Yang of the Urinary Tract – Virginia Perez-Carrasco – Frontiers in Cellular and Infection Microbiology

Vaginal microbiome

Cysteine dependence in Lactobacillus iners constitutes a novel therapeutic target to modify the vaginal microbiota – Seth M. Bloom – bioRxiv

*A type VII secretion system in Group B Streptococcus mediates cytotoxicity and virulence – Brady L Spencer – bioRxiv

Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omics – Zhuye Jie – Genomics, Proteomics & Bioinformatics

Predictive functional analysis reveals inferred features unique to cervicovaginal microbiota of African women with bacterial vaginosis and high-risk human papillomavirus infection – Harris Onywera – PlosOne

Effect of metronidazole on vaginal microbiota associated with asymptomatic bacterial vaginosis – Daniel Ruiz-Perez – Access Microbiology

Oral microbiome

*Dental Biofilm Microbiota Dysbiosis Is Associated With the Risk of Acute Graft-Versus-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation – Vitor Heidrich – Frontiers in Immunology

Fusobacterium nucleatum metabolically integrates commensals and pathogens in oral biofilms – Akito Sakanaka – bioRxiv

Animal microbiome

*Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches – Sharon A. Huws – Microbiome

Animal experiments

A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes – Marion Darnaud – bioRxiv

Bioinformatics

GUNC: detection of chimerism and contamination in prokaryotic genomes – Askarbek Orakov – BMC Genome Biology

metaMIC: reference-free Misassembly Identification and Correction of de novo metagenomic assemblies – Senying Lai – bioRxiv

Open challenges for microbial network construction and analysis – Karoline Faust – The ISME Journal 2021

STRipy: a graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data – Andreas Halman – bioRxiv

Adapting macroecology to microbiology: using occupancy modelling to assess functional profiles across metagenomes – Angus S Hilts – bioRxiv


Webinars &c

Microbiome Virtual International Conference #MVIF – September 14

The International Conference on Group B Strep (ICGBS) – July 20-22

World Enterococcus Day – July 15 – Registration here

BiATA2021 Bioinformatics: from Algorithms to Applications – July 12–15 


LSfM Lecture Series & Workshops : “The Dark Side of Science: Misconduct in Biomedical Research” Dr. Elisabeth Bik – more info here – June 30

EMBARK Webinars – Kimberly Kline “Pathogenesis and persistence during Enterococcus faecalis biofilm-associated infection” and Sofia Forslund “High-throughput measurement of host and microbiota” – EMBARK project – June 30


Writing

Writing and Publishing Scientific Papers: A Primer for the Non-English Speaker – Gábor Lövei – OpenBook Publishers


Art

From Scientist to SciArtist – Eliza Wolfson


June 23, 2021

Happy Wednesday!

Today’s digest includes a review on the microbial transformations of human bile acids as well as research articles focused on extremophiles including Arthrobacter, Acidithiobacillus, and Atribacteria. Also included are a wide variety of preprints on topics such as CRISPR-Cas, the vaginal microbiome, immunocompetence in pigs, the evaluation of RNAlater for preserving field samples for metaproteomics, and more!

Happy reading!

General microbiome

Preprint: CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids – Pinilla-Redondo et al. – bioRxiv

Human respiratory microbiome

Indoor bacterial, fungal and viral species and functional genes in urban and rural schools in Shanxi Province, China–association with asthma, rhinitis and rhinoconjunctivitis in high school students – Fu et al. – Microbiome

Human vaginal microbiome

Preprint: Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data – France et al. – bioRxiv

Human gut microbiome

Review: Microbial transformations of human bile acids – Guzior & Quinn – Microbiome

Preprint: Targeted high-resolution taxonomic identification of Bifidobacterium longum subsp. infantis using human milk oligosaccharide metabolizing genes – Tso et al. – bioRxiv

An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants – Xie et al. – Microbiome

Animal experiments

Preprint: Leveraging host-genetics and gut microbiota to determine immunocompetence in pigs – Ramayo-Caldas et al. – bioRxiv

Joint contributions of the gut microbiota and host genetics to feed efficiency in chickens – Wen et al. – Microbiome

Animal microbiome

Holobiont nitrogen control and its potential for eutrophication resistance in an obligate photosymbiotic jellyfish – Röthig et al. – Microbiome

Plant, root, and soil microbiome

Preprint: Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments – Glass et al. – bioRxiv

Preprint: Seed microbiota revealed by a large-scale meta-analysis including 50 plant species – Simonin et al. – bioRxiv

Preprint: The activity and functions of subarctic soil microbial communities vary across vegetation types – Viitamäki et al. – bioRxiv

Water and extremophile microbiome

Preprint: Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep – Chen et al. – bioRxiv

Preprint: Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures – Li et al. – bioRxiv

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

Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution – Shen et al. – Microbiome

Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs – Sriaporn et al. – Microbiome

Built environment

Preprint: Metagenome-based comparisons of decay rates and host-specificity of fecal microbial communities for improved microbial source tracking – Suttner et al. – bioRxiv

Phages and viruses

Preprint: Expanding clinical phage microbiology: Simulating phage inhalation for respiratory tract infections – Porat et al. – bioRxiv

Techniques

Ultra-accurate microbial amplicon sequencing with synthetic long reads – Callahan et al. – Microbiome

Preprint: Evaluation of RNAlater as a field-compatible preservation method for metaproteomic analyses of bacteria-animal symbioses – Jensen et al. – bioRxiv

Preprint: Predicting microbiome compositions through deep learning – Michel-Mata et al. – bioRxiv

Microbiome and COVID19: some research highlights

Page created on June 20, 2021

Last update: July 4, 2021

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

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

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

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

General and Respiratory Tract Microbiome

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Gut Microbiome studies

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Reviews, hypotheses, and other related topics

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Acknowledgments

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

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

June 19, 2021

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 LabJune 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

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 BriefMicrobiome 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

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 6th, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a variety of interesting papers,in particular for people interested in viromes. The digest contains a really interesting preprint on the diversity of four new Antarctic sea ice bacteriophages, demonstrating their uniqueness and novelty compared to previoulsy characterized phages.

For people interested in bacterial microbiome, this digest contains a lot of very interesting pieces, in particular a very interesting review on the hopes and current limitation of Fecal Microbial Transplants in clinical settings.

Finally, today’s non-microbiology pick is a piece exploring the social impacts of naming diseases using strong-held but flawed names like German measles,

Have a great Weekend!


Human gut microbiome

Impact of the Gut Microbiota Balance on the Health–DiseaseRelationship: The Importance of Consuming Probioticsand Prebiotics – Olvera-Rosales et al. – Foods

Review: Fecal microbiota transplantationin human metabolic diseases:From a murky past to a bright future? – Hanssen et al. – Cell


Animal experiments

Short- and long-term effects of amoxicillin/clavulanic acid or doxycycline on the gastrointestinal microbiome of growing cats – Stavroulaki et al. – BioRxiv

Plant, root, and soil microbiome

Preprint: Deep-rooted plant species recruit distinct bacterial communities in 3 m deep subsoil – Bak et al. – BioRxiV

Preprint: Single seed microbiota: assembly and transmission from parent plant to seedling Chesneau et al. – BioRxiV

Built environment

Reconstruction of metagenome-assembled genomes from aquaria – Ettinger et al. – BiorXiV


Phages and viruses

Viruses roam the wheat phyllosphere – Forero-Junco et al. – BioRxiV

Characteristics of genetically diverse Antarctic sea ice bacteriophages allow adaptation to changing environmental conditions – Demina et al. – BioRxiv

Bioinformatics

Preprint: PGfinder, a novel analysis pipeline for the consistent, reproducible and high-resolution structural analysis of bacterial peptidoglycans – Patel et al. – BioRxiV

Perspective: Computational Viromics: Applications of the Computational Biology in Viromics Studies – Lu and Peng – Virologica Sinica

Preprint: Detecting the hosts of bacteriophages using GCN-Based semi-supervised learning – Shang and Sun – ArxiV


My non-microbiology picks

Preprint: Naming of human diseases on the wrong side of history – Hu – BioRxiV