July 23, 2021

Happy Friday!

It’s an exciting day here because I’m packing for fieldwork! In just a few short days I’ll be sampling from a saline aquifer in Illinois. For those of you who aren’t lucky enough to be going into the field, today’s digest is packed with a wide range of articles. Topics covered include the wild spider gut microbiome, the presence of antibiotic resistance genes in an Ohio river, the mosquito virome, the plant rhizosphere, and more.

Happy reading!

Human gut microbiome

Preprint: Phenotypic and genomic diversification in complex carbohydrate degrading human gut bacteria – Pudlo et al. – bioRxiv

Animal experiments

Effect of biochanin A on the rumen microbial community of Holstein steers consuming a high fiber diet and subjected to a subacute acidosis challenge – Harlow et al. – PLOS ONE

Ear wound healing in MRL/MpJ mice is associated with gut microbiome composition and is transferable to non-healer mice via microbiome transplantation – Velasco et al. – PLOS ONE

Animal microbiome

Preprint: Increased microbial diversity and decreased prevalence of common pathogens in the gut microbiomes of wild turkeys compared to domestic turkeys – Craft et al. – bioRxiv

Interspecific variation and functional traits of the gut microbiome in spiders from the wild: The largest effort so far – Tyagi et al. – PLOS ONE

Plant, root, and soil microbiome

Preprint: Tillage intensity and plant rhizosphere selection shape bacterial-archaeal assemblage diversity and nitrogen cycling genes – Cloutier et al. – bioRxiv

Water and extremophile microbiome

Preprint: An Ohio State Scenic River Shows Elevated Antibiotic Resistance Genes, Including Acinetobacter Tetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent – Murphy – bioRxiv

Biogeochemistry of the Antrim Shale Natural Gas Reservoir – Stemple et al. – ACS Earth and Space Chemistry

Built environment

Preprint: Novel municipal sewage-associated bacterial genomes and their potential in source tracking – Linder et al. – bioRxiv

Preprint: Structure of bacterial communities in Japanese-style bathrooms: Comparative sequencing of bacteria in shower water and showerhead biofilms using a portable nanopore sequencer – Fujiyoshi et al. – bioRxiv

Phages and viruses

Preprint: Dynamic surveillance of mosquitoes and their viromes in Wuhan during 2020 – Ren et al. – bioRxiv

Techniques

Simple mapping-based quantification of a mock microbial community using total RNA-seq data – Moriya – PLOS ONE

Preprint: Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota – Shibata et al. – bioRxiv

July 22, 2021

Human and General Microbiome

The Change Of Gut Microbiota In MDD Patients Under SSRIs Treatment – Yang Shen – Scientific Reports

Minimal-moderate Variation Of Human Oral Virome And Microbiome In IgA Deficiency – Maria José de la Cruz Peña – Scientific Reports

Weight Shapes The Intestinal Microbiome In Preterm Infants: Results Of A Prospective observational study – Fardou H Heida – BMC Microbiology

Functional Heterogeneity In The Fermentation Capabilities Of The Healthy Human Gut microbiota – Thomas Gurry – PloS One

Characterization Of The Blood And Neutrophil-specific Microbiomes And Exploration Of potential bacterial biomarkers for sepsis in surgical patients – Chenyang Wang – Immunity, Inflammation And Disease

Cognitive Function Improvement After Fecal Microbiota Transplantation In In Alzheimer’s dementia patient: a case report – Soo-Hyun Park – Current Medical Research And Opinion

Amplicon And Metagenomic Analysis Of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS – Waleed Aljabr – mSphere

Dental Plaque Microbial Resistomes Of Periodontal Health And Disease And Their Changes after Scaling and Root Planing Therapy – Yutong Kang – mSphere

Archaea Are Rare And Uncommon Members Of The Mammalian Skin Microbiome – Alexander K Umbach – mSystems

Association Between Human Genetic Variants And The Vaginal Bacteriome Of Pregnant Women – Wei Fan – mSystems

Population-wide Diversity And Stability Of Serum Antibody Epitope Repertoires against human microbiota – Thomas Vogl – Nature Medicine

Dynamic Colonization Of Microbes And Their Functions After Fecal Microbiota Transplantation for Inflammatory Bowel Disease – Nathaniel D Chu – mBio

Review: Tryptophan Metabolites Modulate Inflammatory Bowel Disease And Colorectal Cancer By affecting immune system – Moein Ala – International Reviews Of Immunology

Review: From Gut Microbiota To Host Appetite: Gut Microbiota-derived Metabolites As Key regulators – Hui Han – Microbiome

The Roles Of Cytoplasmic Lipid Droplets In Modulating Intestinal Uptake Of Dietary Fat – Alyssa S Zembroski – Annual Reviews Of Nutrition

Review: Intestinal Microbiota In The SARS-CoV-2 Infection: What Is Known? – Patrícia Brito Rodrigues – Advances In Experimental Medicine And Biology

Review: The Microbiota-Gut-Brain Axis And Epilepsy – Qiang Yue – Cellular And Molecular Neurobiology

In Brief: Microbiota Links To Immunotherapy Toxicity – Sarah Seton-Rogers – Nature Reviews Cancer

Opinion: Forming Consensus To Advance Urobiome Research – Linda Brubaker – mSystems

Beneficial Microbes and Compounds

A High-protein Diet Containing Inulin/oligofructose Supports Body Weight Gain associated with lower energy expenditure and carbohydrate oxidation, and alters faecal microbiota in C57BL/6 mice – Franziska Koch – Journal Of Nutritional Science

Immunosuppressive Activity Is Attenuated By Astragalus polysaccharides Via remodeling the gut microenvironment in melanoma mice – Guiqing Ding – Cancer Science

Review: The Interaction Effect Between Tea Polyphenols And Intestinal Microbiota: Role In ameliorating neurological diseases – Mengyu Hong – Journal Of Food Biochemistry

Review: Nutritional Interventions And The Gut Microbiome In Children – Saurabh Mehta – Annual Reviews Of Nutrition

Animal Microbiome and Animal Models

Interspecific Variation And Functional Traits Of The Gut Microbiome In Spiders From the wild: The largest effort so far. – Kaomud Tyagi – PloS One

Vibrio vulnificus Induces The Death Of A Major Bacterial Species In The Mouse Gut via cyclo-Phe-Pro. – Jeong-A Kim – Microbiome

Maternal Cecal Microbiota Transfer Rescues Early-life Antibiotic-induced Enhancement of type 1 diabetes in mice. – Xue-Song Zhang – Cell Host & Microbe

Comprehensive Cultivation Of The Swine Gut Microbiome Reveals High Bacterial Diversity and Guides Bacterial Isolation in Pigs. – Xiaofan Wang – mSystems

Plant Microbiome

Drought Stress And Plant Ecotype Drive Microbiome Recruitment In Switchgrass – Tie-Yuan Liu – Journal Of Integrative Plant Biology

Microbe-dependent Heterosis In Maize – Maggie R Wagner – Proceedings Of The National Academy Of Sciences Of The United States Of America

Review: Prioritizing Host Phenotype To Understand Microbiome Heritability In Plants – Maggie R Wagner – The New Phytologist

Microbiome Analysis and Techniques

On The Robustness Of Inference Of Association With The Gut Microbiota In Stool, rectal swab and mucosal tissue samples – Shan Sun – Scientific Reports

Amplicon Sequence Variants Artificially Split Bacterial Genomes Into Separate Clusters. – Patrick D Schloss – MSphere

Linking Plasmid-based Beta-lactamases To Their Bacterial Hosts Using Single-cell fusion PCR – Peter J Diebold – eLife

An Integrated Machine Learning Framework For A Discriminative Analysis Of schizophrenia using multi-biological data. – Peng-Fei Ke – Scientific Reports

An Intestinal Gut Organ Culture System For Analyzing Host-Microbiota Interactions – Shalhevet Azriel – Journal Of Visualized Experiments (JoVE)

July 15, 2021

Good morning!

There are two particularly exciting papers today; a metagenomic analysis of the genera Akkermansia, providing evidence this is a primarily human microbiota member, and a paper aiming to further understand our knowledge of antibiotic exposure – finding significant alterations in neuronal gene expression in mouse pups.

Human gut microbiome

Development of a prebiotic blend to influence in vitro fermentation effects, with a focus on propionate, in the gut. Collins et al. FEMS Microbiology Ecology.

Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly. Karcher et al. Genome Biology.

Pregnancy and Early life

Effects of early-life penicillin exposure on the gut microbiome and frontal cortex and amygdala gene expression. Volkova et al. iScience.

Animal experiments

Altered milk yield and rumen microbial abundance in response to concentrate supplementation during the cold season in Tibetan sheep. Lin-Sheng Gui et al. Electronic journal of Biotechnology.

Plant, root and soil microbiome

Time outweighs the effect of host developmental stage on microbial community composition. Dibner et al. FEMS Microbiology Ecology.

Food microbiology

Dynamics of dark fermentation microbial communities in the light of lactate and butyrate production. Detman et al. Microbiome.

Bioinformatics

A metabolomics pipeline for the mechanistic interrogation of the gut microbiome. Han et al. Nature.

July 11, 2021

Good morning everyone!

In today’s microbiome digest, we can learn more about the influence of host genetics on the gut microbiome from the research by Laura et. al., and a perspective by Liliana et. al. Also, this digest contains interesting methods/tools/pipelines such as a Robust covariance estimation method by Yong He et. Al., a new pipeline for structural characterization and classification of RNA-Seq microbiome data by Racedo et. Al, and a k-mer based tool ‘kASA’ for taxonomic analysis of metagenomic data.

Enjoy reading. Happy Sunday.

General microbiome

Review: Non-zero-sum microbiome immune system interactions – Timur Tuganbaev – European Journal of Immunology

Review: Intersection of FcγRIIB, the microbiome, and checkpoint inhibitors in antitumor immunity – Kirsten M. Baecher – Cancer Immunology, Immunotherapy

Evaluating extraction methods to study canine urine microbiota – Ryan Mrofchak – PLOS ONE

Gut microbiome

Review: The potential of outdoor environments to supply beneficial butyrate-producing bacteria to humans – Joel E. Brame – Science of The Total Environment

Gut microbiome heritability is nearly universal but environmentally contingent – Laura Grieneisen – Science

Perspective: Host genetics influence the gut microbiome– Liliana Cortes-Ortiz – Science

Isoflavone diet ameliorates experimental autoimmune encephalomyelitis through modulation of gut bacteria depleted in patients with multiple sclerosis – Samantha N. Jensen – Science Advances

Skin microbiome

Monitoring Infection and Antibiotic Treatment in the Skin Microbiota of Farmed European Seabass (Dicentrarchus Labrax) Fingerlings – Daniela Rosado – Microbial Ecology

Respiratory microbiome

Metagenomic Next-Generation Sequencing for the Diagnosis of Pneumocystis jirovecii Pneumonia in Non-HIV-Infected Patients: A Retrospective Study – Juan Jiang – Infectious Diseases and Therapy

Optimal primer selection for sinus microbiome profiling: A comparative analysis of the V1-V3 and V3-4 16S target regions – James Connell – International forum of Allergy and Rhinology

Detection of Chlamydia psittaci in both blood and bronchoalveolar lavage fluid using metagenomic next-generation sequencing – Yuan, Yingpu – Medicine

Animal microbiome / Animal experiments

Review: New insights into the microbiota of wild mice – Ho-Keun Kwon – Mammalian Genome

Bacterial communities of indoor surface of stingless bee nests – Leandro Pio de Sousa – PLOS ONE

Elucidating the optimum added dosage of Diatomite during co-composting of pig manure and sawdust: Carbon dynamics and microbial communityXiunaRen – Science of The Total Environment

Punicic acid ameliorates obesity and liver steatosis by regulating gut microbiota composition in mice – Gaofeng Yuan – Food and Function

Arc1 and the microbiota together modulate growth and metabolic traits in Drosophila – Scott A. Keith – Development

Plant, root and soil microbiome

Diversity and Interactomics of Bacterial Communities Associated with Dominant Trees During Tropical Forest Recovery – Angel A. Becerra-Lucio – Current Microbiology

Land-use types shape soil microbial compositions under rapid urbanization in the Xiong’an New Area, China – Can Wang – Science of The Total Environment

Insights into the Endophytic Bacterial Microbiome of Crocus sativus: Functional Characterization Leads to Potential Agents that Enhance the Plant Growth, Productivity, and Key Metabolite Content – Tanveer Ahmad – Microbial Ecology

Using a high-throughput sequencing technology to evaluate the various forage source epiphytic microbiota and their effect on fermentation quality and microbial diversity of Napier grass – Niaz Ali – Archives of Microbiology

Global homogenization of the structure and function in the soil microbiome of urban greenspaces – Manuel Delgado-Baquerizo – Science Advances

Water microbiome

Anaerobic fermentation of hydrothermal liquefaction wastewater of dewatered sewage sludge for volatile fatty acids production with focuses on the degradation of organic components and microbial community compositions – Zheng Chen – Science of The Total Environment

Methods/Tools/Pipelines

Robust covariance estimation for high-dimensional compositional data with application to microbial communities analysis – Yong He – Statistics in Medicine

A new pipeline for structural characterization and classification of RNA-Seq microbiome dataSebastian Racedo – BioData Mining.

Taxonomic analysis of metagenomic data with kASA – Silvio Weging – Nucleic Acids Res

Rapid and simultaneous determination of histidine metabolism intermediates in human and mouse microbiota and biomatrices – Inmaculada Acuña – Biofactors

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 4, 2021

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

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 18, 2021

Review articles on exciting microbiome topics dominate today’s post. My personal favorite review is by Berthoud et al. on gut-brain communication with focus on understanding functions of the vagus nerve. Others include – rumen microbiome, gut microbiota in neuronal feeding circuits, gut-brain axis in gastrointestinal cancer and a beautiful snapshot illustrating summary of microbiota effects on host physiology. Happy reading!

General Microbiome

Gut microbiota as a transducer of dietary cues to regulate host circadian rhythms and metabolism – Hyoann Choi – Nature Reviews Gatsroenterology and Hepatology

SnapShot: Microbiota effects on host physiology – Jennifer H.Hill – Cell

Roles for the gut microbiota in regulating neuronal feeding circuits – Kristie B. Yu – Journal of Clinical Investigation

Gut-brain communication and obesity: understanding functions of the vagus nerve – Hans-Rudolf Berthoud – Journal of Clinical Investigation

Exploiting unique features of the gut-brain interface to combat gastrointestinal cancer – Alyssa Schledwitz – Journal of Clinical Investigation

Human Microbiome

Evaluation of saliva as a source of accurate whole‐genome and microbiome sequencing data – Anthony F. Herzig – Genetic Epidemiology

The effects of nondigestible fermentable carbohydrates on adults with overweight or obesity: a meta-analysis of randomized controlled trials – Bocheng Xu – Nutrition Reviews

Altered gut microbiota correlates with cognitive impairment in Chinese children with Down’s syndrome – Shimeng Ren – European Child & Adolescent Psychiatry

A synthetic consortium of 100 gut commensals modulates the composition and function in a colon model of the microbiome of elderly subjects – Marta Perez – Gut Microbes

Animal Microbiome

The rumen microbiome: balancing food security and environmental impacts – Itzhak Mizrahi – Nature Reviews Microbiology

Components of the Gut Microbiome that Influence Bone Tissue‐Level Strength – Marysol Luna – Journal of Bone and Mineral Research

Characterization of growth phenotypes and gastrointestinal tract microbiota in sheep fed with caragana – Ke Zhang – Journal of Applied Microbiology

Techniques

‘GutFeel’: an in silico method for predicting gut health status based on the metabolic functional capabilities of the resident microbiome – Swadha Anand – Febs Letters

MiMeNet: Exploring microbiome-metabolome relationships using neural networks – Derek Reiman – Plos Computational Biology

Bacteria

Anatomy promotes neutral coexistence of strains in the human skin microbiome – Arolyn Conwill – BioRxiv

May 10, 2021

Good morning! Today’s papers are mainly focused on the gut microbiota. A particular highlight is Li et al’s study, involving a network analysis of ulcerative colitis patient microbiotas, showing their potential role as opportunistic pathogens. Enjoy!

Gut microbiome

Iron status influences non-alcoholic fatty liver disease in obesity through the gut microbiome. Mayneris-Perxachs et al. Microbiome.

Ecological and network analyses identify four microbial species with potential significance for the diagnosis/treatment of ulcerative colitis (UC). Li et al. BMC microbiology.

A meta-analysis of Gut Microbiota in Children with Autism. Andreo-Martinéz et al. Journal of autism and developmental disorders.

Pregnancy and early life

Deviations in the gut microbiota of neonates affected by maternal group B Streptococcus colonization. Li et al. BMC microbiology.

Animal experiments

Preprint: Longitudinal changes in diet cause repeatable and largely reversible shifts in gut microbial communities of laboratory mice and are observed across segments of the entire intestinal tract. Low et al. Bioxriv.

Cage environment regulates gut microbiota independent of toll-like receptors. Lipinski et al. Infection and Immunity.

Changes of gut microbiome composition and metabolites associated with hypertensive heart failure rats. Li et al. BMC microbiology.

Plant, root and soil microbiome

Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field. Cadot et al. Microbiome.

Water and Extremophile Microbiome

Preprint: A metagenomic view of novel microbial and metabolic diversity found within the deep terrestrial biosphere. R. Osburn et al. Bioxriv.

Bioinformatics

geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response. Minot et al. Genome Biology.

May 4, 2021

In today’s post – host-microbe marker for inflammatory bowel disease, evolution of soil bacterium along the climate gradient, how C. difficile exploits host metabolite under inflammatory conditions induced by its own toxins and differential response of commensals to alter C. difficle virulence.

Job Posting

Microbiome Scientific Researcher, Computational (Cancer Immunology) – Genentech South San Francisco, California

General Microbiome

Endothelium–gut communication: IGF‐1Rs crosstalk with microbiota – Zhen Bouman Chen – EMBO reports

Recent advances in marine algae oligosaccharides: structure, analysis, and potential prebiotic activities – Xu-Ting Xie – Critical Reviews in Food Science and Nutrition

Human Microbiome

Interplay between diet and gut microbiome, and circulating concentrations of trimethylamine N-oxide: findings from a longitudinal cohort of US men – Jun Li – Gut

Gut Dysbiosis Associated with Antibiotics and Disease Severity and Its Relation to Mortality in Critically Ill Patients – Masahiro Ojima – Digestive Diseases and Sciences

Effects of Totum-63 on glucose homeostasis and post-prandial glycemia: a translational study – Vivien Chavanelle – American Journal of Physiology Endocrinology and Metabolism

Impact of a fermented soy beverage supplemented with acerola by-product on the gut microbiota from lean and obese subjects using an in vitro model of the human colon – Antonio Diogo Silva Vieira – Environmental biotechnology

Decoding the matrix: multiomics reveals host-microbe biomarker for inflammatory bowel disease – Monica Viladomiu – The Journal of Clinical Investigation

Animal Microbiome

C. difficile exploits a host metabolite produced during toxin-mediated disease – Kali M. Pruss – Nature

In vivo commensal control of Clostridioides difficile virulence – Brintha P. Girinathan – BioRxiv

Description and comparison of the skin and ear canal microbiota of non-allergic and allergic German shepherd dogs using next generation sequencing – Neoklis Apostolopoulos – PlosOne

Plant, root and soil microbiome

Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient – Alexander B. Chase – PNAS

Soils and sediments host novel archaea with divergent monooxygenases implicated in ammonia oxidation – Spencer Diamond – BioRxiv

Water microbiome

Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem – Ya-Jou Chen – ISME Journal

Techniques

Comprehensive single‐PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S – Yi‐Chun Yeh – Environmental Microbiology

Bacteria

Completion of the gut microbial epi-bile acid pathway – Heidi L. Doden – Gut Microbes

Possible effects of Porphyromonas gingivalis on the blood-brain barrier in Alzheimer’s disease – Ingar Olsen – Expert Review of Anti-infective Therapy

Population genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii – Tao Luo – Nature Communications