September 1, 2020

Today’s post consists of review article on short chain fatty acids, research articles on efficacy of fecal microbiota transplant in patients with C. difficle infection and comorbities, identification of potential microbial biomarkers for preterm birth and a new technique to perform ultrafast microbial community analysis. Happy reading!

General microbiome

A systematic review of the effect of dietary pulses on microbial populations inhabiting the human gut – C.P.F. Marinangeli – Beneficial Microbes

Short chain fatty acids in human gut and metabolic health – E E Blaak – Beneficial Microbes

Human microbiome

The gut microbiome–derived metabolite trimethylamine N-oxide modulates neuroinflammation and cognitive function with aging – Vienna E. Brunt – Geroscience

Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial – Suryang Kwak – Microbiome

Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in Patients With Multiple Comorbidities: Long-Term Safety and Efficacy Results From a Tertiary Care Community Hospital – Charumathi Raghu Subramanian – Gastroenterology Research

Gut commensal microbiota and decreased risk for Enterobacteriaceae bacteriuria and urinary tract infection – Matthew Magruder – Gut Microbes

Leveraging sequence‐based faecal microbial community survey data to identify alterations in gut microbiota among patients with Parkinson’s disease – Tianyi Ji – European Journal of Neuroscience

Plasma enterobacterial ClpB levels and ClpB- and α-MSH–reactive immunoglobulins in lung cancer patients with and without anorexia – Alessio Molfino – Nutrition

Identification of Potential Biomarkers in the Cervicovaginal Fluid by Metabolic Profiling for Preterm Birth – AbuZar Ansari – Metabolites

Plant microbiome

Suppression of rice planthopper populations without affecting the rice microbiota by the entomopathogenic fungus Metarhizium anisopliae – Yifan Peng – Applied and Environmental Microbiology

Cold Plasma Treatment of Sunflower Seeds Modulates Plant-Associated Microbiome and Stimulates Root and Lateral Organ Growth – Inga Tamošiūnė – Frontiers in Plant Science

Water microbiome

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments – Da-Shuai Mu – Microbiome

Techniques

Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2 – Jennifer Lu – Microbiome

Non-microbiology picks

Clinical characteristics of children and young people hospitalised with covid-19 in the United Kingdom: prospective multicentre observational cohort study – Olivia V Swann – BMJ

August 12, 2020

General microbiome

[REVIEW] Host–microbiota interactions in immune-mediated diseases – Ruff, Greiling and Kriegel – Nature Reviews Microbiology

[REVIEW] Diversity within species: interpreting strains in microbiomes – van Rossum et al. – Nature Reviews Microbiology

Animal microbiome

Vast Differences in Strain-Level Diversity in the Gut Microbiota of Two Closely Related Honey Bee Species – Ellegaard et al. – Current Biology

Oral and vaginal microbiota in selected field mice of the genus Apodemus: a wild population study – Matejkova et al. – Scientific Reports

Characterization of Cutaneous Bacterial Microbiota from Superficial Pyoderma Forms in Atopic Dogs – Older et al. – Pathogens

Water and extremophile microbiome

Cryptic fungal diversity revealed in deep- sea sediments associated with whale-fall chemosynthetic ecosystems – Nagano et al. – Mycology

Bioinformatics

[PREPRINT] Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization – Goren et al. – bioarxiv

A Distance-Based Framework for the Characterization of Metabolic Heterogeneity in Large Sets of Genome-Scale Metabolic Models – Cabbia et al. – Patterns

FORENSIC: an Online Platform for Fecal Source Identification – Roguet et al. – mSystems

Techniques

Bacterial mock communities as standards for reproducible cytometric microbiome analysis – Cichocki et al. – Nature Protocols

July 30, 2020

Hello from Lübeck! This week started slowly but our todays post covers quite a range of topics with a couple of reviews about our understanding of the gut microbiome related to digestive diseases. Of particular note is a publication by Kadosh et al. (Nature 2020) linking the gut microbiome and p53 in mice. This highlights the role of the microenvironment on cancer in general.

● Human vaginal microbiome

Changes in the vaginal microbiota following antibiotic treatment for Mycoplasma genitalium, Chlamydia trachomatis and bacterial vaginosis – Ahrens et al. – Plos One

● Human gut microbiome

[REVIEW] Gut Microbiome Modulates Response to Cancer Immunotherapy – Khan et al. – Digestive Diseases and Sciences

[REVIEW] Healthy Human Gastrointestinal Microbiome: Composition and Function After a Decade of Exploration – Ruan et al. – Digestive Diseases and Sciences

[REVIEW] Microbiome and Its Role in Irritable Bowel Syndrome – Pimentel and Lembo – Digestive Diseases and Sciences

[REVIEW] Diet and Gut Microbes Act Coordinately to Enhance Programmed Cell Death and Reduce Colorectal Cancer Risk – Chapkin et al. – Digestive Diseases and Sciences

Diversity of Gut Microbiota and Bifidobacterial Community of Chinese Subjects of Different Ages and from Different Regions – Yang et al. – Microorganisms

[PREPRINT] Gut Microbiota Changes in Nonalcoholic Fatty Liver Disease and Concomitant Cardiovascular Diseases – Kurinna – bioarxiv

Lactobacillus plantarum-Mediated Regulation of Dietary Aluminum Induces Changes in the Human Gut Microbiota: an In Vitro Colonic Fermentation Study – Yu et al. – Probiotics and Antimicrobial Proteins

Troublesome friends within us: the role of gut microbiota on rheumatoid arthritis etiopathogenesis and its clinical and therapeutic relevance – Reyes-Castillo et al. – Clinical and Experimental Medicine

Duodenal Microbiota in Stunted Undernourished Children with Enteropathy – Chen et al. – The New Englang Journal of Medicine

Small molecules, big effects: microbial metabolites in intestinal immunity – Glotfelty, Wong and Levy – AJP Gastrointestinal and Liver Physiology

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic – Kadosh et al. – Nature

Impact of PepT1 deletion on microbiota composition and colitis requires multiple generations – Viennois et al. – npj Biofilms and Microbiomes

Plant, root, and soil microbiome

[REVIEW] Recent advances in the role of plant metabolites in shaping the root microbiome – Jacoby et al. – F1000

Food microbiology

Selection of cereal-sourced lactic acid bacteria as candidate starters for the baking industry – Milanovic et al. – Plos One

The sources and transmission routes of microbial populations throughout a meat processing facility – Zwirzitz et al. – npj Biofilms and Microbiomes

Phages and viruses

[PREPRINT] Characterization of the gut DNA and RNA viromes in a cohort of Chinese residents and visiting Pakistanis – Yan – bioarxiv

Bioinformatics

[REVIEW] Tools for Analysis of the Microbiome – Galloway-Pena and Hanson – Digestive Diseases and Sciences

Techniques

Microbial community dissimilarity for source tracking with application in forensic studies – Carter et al. – Plos One

Microbes in the news

Pilot study examines facial microbiome diversity – Petrou – Dermatology Times

The 2020 Way To Treat Your Skin Is All About Bacteria, Bugs And Microbiomes – Driver – ELLE

July 29, 2020

● General microbiome

[REVIEW] The dialogue between unconventional T cells and the microbiota – Lin et al. – Mucosal Immunology

Human skin microbiome

Stability of Skin Microbiome at Sacral Regions of Healthy Young Adults, Ambulatory Older Adults, and Bedridden Older Patients After 2 Years – Ogai et al. – Biological Research For Nursing

The skin microbiome as a clinical biomarker in atopic eczema: Promises, navigation, and pitfalls – Reiger et al. – Journal of Allergy and Clinical Immunology

● Human gut microbiome

Feeding Bugs to Bugs: Edible Insects Modify the Human Gut Microbiome in an in vitro Fermentation Model – Young et al. – Front. Microbiol.

● Plant, root, and soil microbiome/metabolome

[REVIEW] The Application of Metabolomics for the Study of Cereal Corn (Zea mays L.) – Lena Gálvez Ranilla – Metabolites

Elevational is the main factor controlling the soil microbial community structure in alpine tundra of the Changbai Mountain – Tang et al. – Scientific Reports

● Techniques

A guide to deciphering microbial interactions and metabolic fluxes in microbiome communities – Maciek R Antoniewicz – Current Opinion in Biotechnology

July 10, 2020

Today’s digest contains many exciting articles – gut microbiome in precision medicine for cancer, important review on patent protection in microbiome therapeutics, role of the gut microbiota in sympathetic neurons, interaction of pacemaker neurons with the gut microbiota, gut dysbiosis in lupus and many more….Enjoy reading and happy weekend!

General microbiome

Gut microbiome, big data and machine learning to promote precision medicine for cancer – Giovanni Cammarota – Nature Reviews Gastroenterology and Hepatology

Co-evolution and Co-speciation of Host-Gut Bacteria Systems – Mathieu Groussin – Cell Host and Microbe

Microbiome therapeutics and patent protection – Mark J. FitzGerald – Nature Biotechnology

Human microbiome

Fecal Microbiota Transplantation is Safe and Effective in Patients with Clostridioides difficile Infection and Cirrhosis – Yao-WenCheng – CLinial Gastroenterology and Hepatology

Association of Gut Microbiota-Dependent Metabolite Trimethylamine N-Oxide with First Ischemic Stroke – Taoping Sun – Journal of Atherosclerosis and Thrombosis

Dietary Strategies for Maintenance of Clinical Remission in Inflammatory Bowel Diseases: Are We There Yet? – Konstantinos Gkikas – Nutrients

The duodenal microbiome is altered in small intestinal bacterial overgrowth – Gabriela Leite – PlosOne

Faecal microbiota transplantation: A life-saving therapy challenged by commercial claims for exclusivity – Christian LodbergHvas – EClinical Medicine

Animal experiments

Microbiota modulate sympathetic neurons via a gut–brain circuit – Paul A. Muller – Nature

Prototypical pacemaker neurons interact with the resident microbiota – Alexander Klimovich – PNAS

Gut microbiota dysbiosis and altered tryptophan catabolism contribute to autoimmunity in lupus-susceptible mice – Seung-Chul Choi – Science Translational Medicine

The relationship between gut microbiota and short chain fatty acids in the renal calcium oxalate stones disease – Yu Liu – Faseb Journal

Sodium Butyrate Alleviates Mouse Colitis by Regulating Gut Microbiota Dysbiosis – Xiujing Dou – Animals

Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome – Min-Ting Lee – Journal of Lipid Research

Commentary: Modulating microbiome metabolites in vivo – Chun-Jun Guo – Science

Plant, root and soil microbiome

Quantitative comparison between the rhizosphere effect of Arabidopsis thaliana and co-occurring plant species with a longer life history – Martinus Schneijderberg – ISME Journal

Water microbiome

Anthropogenic dissolved organic carbon and marine microbiomes – Maria Vila-Costa – ISME Journal

Functional foods

Effect of a functional fibre supplement on glycemic control when added to a year-long medically supervised weight management program in adults with type 2 diabetes – Raylene A. Reimer – European Journal of Clinical Nutrition

Prenatal exposure to the probiotic Lactococcus lactis decreases anxiety-like behavior and modulates cortical cytoarchitecture in a sex specific manner – Natalia Surzenko – PlosOne

Non microbiology picks

SARS-CoV-2 is transmitted via contact and via the air between ferrets – Mathilde Richard – Nature Communications

July 7, 2020

Today’s digest features the mighty sourdough microbiome, AGNOSTOS (a computational workflow for genes annotation using clustering and remote homology detection, contextualizing them with genomic and environmental information), and a new episode of the Bioinformatics Chat podcast about reproducible pipelines and NGLess (a user-friendly domain-specific programming language for NGS data processing), and more. Happy reading/listening!

General microbiome

Microbiome definition re-visited: old concepts and new challenges – Gabriele Berg – Microbiome

Positive interactions are common among culturable bacteria – Jared Kehe – bioRxiv

Gut microbiome

An emerging role of Prevotella histicola on estrogen-deficiency induced bone loss through the gut microbiota-bone axis – Zhongxiang Wang – bioRxiv

Identifying novel high-impact rare disease-causing mutations, genes and pathways in exomes of Ashkenazi Jewish inflammatory bowel disease patients – Yiming Wu – medRxiv

Early prediction of liver disease using conventional risk factors and gut microbiome-augmented gradient boosting – Yang Liu – medRxiv

GWAS of stool frequency reveals genes, pathways, and cell types relevant to human gastrointestinal motility and irritable bowel syndrome – Ferdinando Bonfiglio – medRxiv

Relationships of gut microbiota, short-chain fatty acids, inflammation, and the gut barrier in Parkinson’s disease – Velma Aho – medRxiv

Lung microbiome

Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung – Adrian Kordes – Nature Communications

Genitourinary microbiome

Architecture and function of human uromodulin filaments in urinary tract infections – Gregor L. Weiss – Science

The structure and diversity of strain level variation in vaginal bacteria – Brett A. Tortelli – bioRxiv

Synchronous genitourinary lichen sclerosus signals a distinct urinary microbiome profile in men with urethral stricture disease – Andrew J. Cohen – World Journal of Urology

Human urine 1H NMR metabolomics reveals alterations of the protein and carbohydrate metabolism when comparing habitual Average Danish diet vs. healthy New Nordic diet – Alessia Trimigno – Nutrition

Animal experiments

Lactobacillus rhamnosus probiotic prevents airway function deterioration and promotes gut microbiome resilience in a murine asthma model – Irina Spacova – Gut Microbes

Food microbiome

*The Sourdough Microbiome – Justine Dees – ASM

Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function – Brittany A. Niccum – mSystems

Bioinformatics

*Light into the darkness: Unifying the known and unknown coding sequence space in microbiome analyses – Chiara Vanni – bioRxiv

Welcome to the dark side of genomes and metagenomes – a blog post about the above mentioned study – Antonio Fernandez-Guerra

GraphBin: refined binning of metagenomic contigs using assembly graphs – Vijini Mallawaarachchi – Bioinformatics

Podcast

*Reproducible pipelines and NGLess with Luis Pedro Coelho – Roman Cheplyaka – The Bioinformatics Chat

June 22, 2020

General microbiome
Impact of feeding and stirring regimes on the internal stratification of microbial communities in the fermenter of anaerobic digestion plants – Robert Heyera – Bioresource Technology

Human microbiome
REVIEW: Role of the Microbiome in Allergic Disease Development – Andrea C. Aguilera, – Pediatric Allergy and Immunology

Optimization and standardization of the culturomics technique for human microbiome exploration – Ami Diakite – Scientific Reports

Human skin microbiome
The microbiome of diabetic foot ulcers: a comparison of swab and tissue biopsy wound sampling techniques using 16S rRNA gene sequencing – J. Travis – BMC Microbiology

Human gut microbiome
Interpersonal Gut Microbiome Variation Drives Susceptibility and Resistance to Cholera Infection – Salma Alavi – Cell

EDITORIAL: Gut microbes effects on host metabolic alterations in health and disease – Suzana D. Savkovic – Gut Microbes

Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study – Mohammad Tahseen Al Bataineh – Scientific Reports

Alterations in the Gut Microbiome in the Progression of Cirrhosis to Hepatocellular Carcinoma – Yelena Lapidot – mSystems

Human respiratory microbiome
Taxonomic diversity of sputum microbiome in lung cancer patients and its relationship with chromosomal aberrations in blood lymphocytes – V. G. Druzhinin – Scientific Reports

Pregnancy and early life
Human milk microbiota development during lactation and its relation to maternal geographic location and gestational hypertensive status – Yi Wan – Gut Microbes

Maternal Microbiota, Cortisol Concentration, and Post-PartumWeight Recovery Are Dependent on Mode of Delivery – Marta Selma-Royo – Nutrients

Human ancient microbiome
Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia – Anna Philips – BMC Genomics

Animal experiments
Zebrafish microbiome studies make waves – Keaton Stagaman – Lab Animal

Animal microbiome
An Insight into Diversity and Functionalities of Gut Microbiota in Insects – Shengchen Wang – Current Microbiology

Plant, root, and soil microbiome
Microbial assimilation dynamics differs but total mineralization from added root and shoot residues is similar in agricultural Alfisols – Yingde Xu – Soil Biology and Biochemistry

Effects of increasing concentrations of unamended and gypsum modified bauxite residues on soil microbial community functions and structure – A mesocosm study – Camille Fourrier – Ecotoxicology and Environmental Safety

Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables – Peter Kusstatscher – FEMS Microbiology Ecology

Variations of rhizospheric soil microbial communities in response to continuous Andrographis paniculata cropping practices – Junren Li – Botanical Studies

Seed Metabolism and Pathogen Resistance Enhancement in Pisum sativum During Colonization of Arbuscular Mycorrhizal Fungi: An Integrative Metabolomics-Proteomics Approach – Nima Ranjbar Sistani – Frontiers in Plant Science

Water microbiome
Differential Responses of a Coastal Prokaryotic Community to Phytoplanktonic Organic Matter Derived from Cellular Components and Exudates – Hiroaki Takebe – Microbes and Environments

Built environment
MINI-REVIEW: Microorganisms populating the water-related indoor biome – Monika Novak Babič – Applied Microbiology and Biotechnology

Pre-print
Shotgun metagenomics reveals signicant gut microbiome features in different grades of acute pancreatitis – Shanshan Yu – Research Square

Characteristics of Esophagus Flora in Patients with Esophageal Squamous Cell Carcinoma in Central China – Shuixiang He – Research Square

Can root-associated fungi mediate the impact of abiotic conditions on the growth of a High Arctic herb? – Magdalena Wutkowska – bioRxiv

Microbes on the market
Finch Therapeutics Announces Positive Topline Results from Randomized Controlled Trial of CP101, an Oral Microbiome Drug, for the Prevention of Recurrent C. difficile Infection – Finch Therapeutics

Microbes in the news
Gut reaction: How the gut microbiome may influence the severity of COVID-19 – Shirin Moossavi – The Conversation

Towards virtual physiological humans: integrating metabolism, physiology, and gut-microbiome

Science communication on a recently published paper


Precision Medicine

A milestone in precision medicine would be the ability to explore generative models that can capture the real-world complexity of human physiology. If computational models can successfully integrate physiology, metabolism, and host-microbiome data – thereby achieving personalization of predictive models of virtual physiological humans – this would be a key stepping-stone in yielding promising therapeutic targets that are both individual-specific and case-specific. Thus, the science (and art) of generating and exploring virtual physiological humans could be a boon to systems physiology and precision medicine.

Whole-body metabolic reconstructions

Towards this end, Thiele et al. recently published an intriguing paper. Thiele et al. demonstrate building and validation of sex-specific curated Whole-Body Metabolic (WBM) reconstructions. Computational models derived from such WBM reconstructions offer a novel molecular-level, anatomically and physiologically consistent, sex-specific genome-scale reconstructions of human physiology and metabolism. Thiele et al. further demonstrated that the WBM reconstructions can be ‘personalized’ via integration of quantitative physiological data with multi-omics such as metabolomics, and gut-microbiome. Thus, Thiele et al. introduce Harvey and Harvetta, the male and female WBM reconstructions, respectively. These reconstructions and the derived models and analysis enable novel assessment of, e.g., host-microbiome co-metabolism that is individual-specific and is resolved at an organ-level.

Complexity

The extreme complexity of real-world metabolic modelling of host-microbiome in humans can hardly be overstated. Thiele et al. address this critical challenge via constraint-based reconstruction – their models account for the enormous diversity of microbiome-associated microbial genes that are meaningful both physiologically and is individual-specific such as in host-microbiome co-metabolism. Thus this approach allows case-specific investigation of human metabolism, such as for studying inherited metabolic diseases.

Approach

Previously the Thiele Lab , extensive metabolic modelling of metabolic and physiologically relevant pathways (curated algorithmically and manually) led to a comprehensive model that allows investigation via constraint-based reconstruction of over 80,000 pathways. Thiele et al. approached the problem into a smaller sub-problems that they have previously addressed. First – by compiling organ-specific information from previous literature and including experimental-omics data, Thiele Lab generated WBM reconstructions. Second – Thiele Lab imposed constraints the WBM reconstructions via (large-scale) physiology, dietary constraints and quantitative metabolomic data.

Highlights

A key challenge that Thiele et al. addressed in this current 2020 paper is the integration of more than 80,000 biochemical reactions, that were both anatomically and physiologically consistent. These WBM reconstructions describe 26 organs and 6 blood cell types and capture whole-body organ-resolved metabolism. Importantly, these recapitulate previously known inter-organ metabolic cycles and energy use. Interestingly, WBM models can also predict biomarkers. This might, e.g., elucidate new pathways or targets that are implicated in heritable metabolic diseases.

Take-home-message and future ahead

Exploring such quantitative metabolic models could reveal new molecular insights pertaining to (co-dependence of host-microbiome) metabolism and overall human physiology and homeostasis – both in health and disease. The power of computational models is further exemplified if these allow addressing questions via novel hypothesis-testing that go beyond the scope of wet-lab experiments.


written by: Div Prasad

I’m interested in quantitative biology (at the intersection) of human genetics, machine learning, and host-microbiome interactions.

Twitter: @divyaePrasad
github: divprasad

June 5, 2020

Today’s digest features a review on genetic variability within species in microbiomes, a study on Lactobacilli in the human nose, a new episode of Microbiology Lab Pod with the latest science news on functional metagenomics, a novel resistance gene called GAR, and more. Happy reading/listening!

General microbiome

*Diversity within species: interpreting strains in microbiomes – Thea Van Rossum – Nature Reviews

Earth microbial co-occurrence network reveals interconnection pattern across microbiomes – Bin Ma – Microbiome

Oral and nasal microbiome

Local oral and nasal microbiome diversity in age-related macular degeneration – Jacob Rullo – Scientific Reports

*Lactobacilli Have a Niche in the Human Nose – Ilke De Boeck – Cell Reports

Gut microbiome

Resistant maltodextrin intake reduces virulent metabolites in the gut environment: randomized control study in a Japanese cohort – Yuichiro Nishimoto – MedRxiv

Pregnancy and early life

One year cross-sectional study in adult and neonatal intensive care units reveals the bacterial and antimicrobial resistance genes profiles in patients and hospital surfaces – Ana Paula Christoff – PlosOne

Animal microbiome

Cecal microbiome composition and metabolic function in probiotic treated broilers – Denise R. Rodrigues – PlosOne

Characterization of native Escherichia coli populations from bovine vagina of healthy heifers and cows with postpartum uterine disease – Candelaria Gonzalez Moreno – PlosOne

Animal experiments

Structural and Functional Changes of Gut Microbiota in Ovariectomized Rats and Their Correlations With Altered Bone Mass – Sicong Ma – Aging

Plant, root, and soil microbiome

Dissecting the effect of continuous cropping of potato on soil bacterial communities as revealed by high-throughput sequencing – Jing Zhao – Plos One

Water microbiome

Increasing flow rate reduces biofouling and colonization by filamentous bacteria in drippers fed with reclaimed wastewater – Kevin Lequette – bioRxiv

Phages and viruses

Integration of phage and yeast display platforms: A reliable and cost effective approach for binning of peptides as displayed on-phage – Priyanka Pandya – PlosOne

Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes – Kira Moon – Microbiome

Bioinformatics

Estimating Microbial Interaction Network: Zero-inflated Latent Ising Model Based Approach– Jie Zhou – bioRxiv

Assessment of statistical methods from single cell, bulk RNA-seq and metagenomics applied to microbiome data – Matteo Calgaro – bioRxiv

Metabolomics

Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power– Jasmin Hafner – Synthetic Biology

Inferring Active Metabolic Pathways from Proteomics and Essentiality Data – Ariadna Montero-Blay – Cell Reports

Podcast

*May 2020 Pod: Discovering novel resistance genes and how bacteria become virulent – Bengtsson-Palme Lab and Marlies Böhm – Microbiology Lab Pod

June 3, 2020

Today’s post covers articles on role of microbiome in sepsis, early life microbiota related to cystic fibrosis and respiratory syncitial virus disease, promise and challenge with cancer microbiome, effect of probiotics on intestinal homeostasis after chemotherapy and many more!

General microbiome

Predictive biology: modelling, understanding and harnessing microbial complexity – Allison J. Lopatkin – Nature Reviews Microbiology

The Gut Microbiome’s Role in the Development, Maintenance, and Outcomes of Sepsis – Max W Adelman – Critical Care

The Promise and Challenge of Cancer Microbiome Research – Sumeed Syed Manzoor – Genome Biology

Antidiabetic Effects of Flavan-3-ols and Their Microbial Metabolites – Estefanía Márquez Campos – Nutrients

Human microbiome

Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome – Roie Levy – PNAS

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale – Soumaya Zlitni – Genome Medicine

Comparative Assessment of Faecal Microbial Composition and Metabonome of Swine, Farmers and Human Control – Shiang Chiet Tan – Scientific Reports

Matching Between Donors and Ulcerative Colitis Patients Is Important for Long-Term Maintenance After Fecal Microbiota Transplantation – Koki Okahara – Journal of Clinical Medicine

Preganancy and early life

Alterations in Vaginal Microbiota and Associated Metabolome in Women With Recurrent Implantation Failure – Min Fu – mBio

Development of the Gut Microbiota in Early Life: The Impact of Cystic Fibrosis and Antibiotic Treatment – Maartje Kristensen – Journal of Cystic Fibrosis

Altered Gut Microbiota in Infants Is Associated With Respiratory Syncytial Virus Disease Severity – Jeffrey N Harding – BMC Microbiology

Ecological Succession in the Vaginal Microbiota During Pregnancy and Birth – M A Rasmussen – Isme Journal

Animal experiments

Host genotype and exercise exhibit species-level selection for members of the gut bacterial communities in the mouse digestive system – R. A. Dowden – Scientific Reports

Repetitive, Mild Traumatic Brain Injury Results in a Progressive White Matter Pathology, Cognitive Deterioration, and a Transient Gut Microbiota Dysbiosis – Mariana Angoa-Pérez – Scientific Reports

Association of Gut Microbiota Composition and Function With an Aged Rat Model of Senile Osteoporosis Using 16S rRNA and Metagenomic Sequencing Analysis – Sicong Ma – Aging

Increasing the Hindgut Carbohydrate/Protein Ratio by Cecal Infusion of Corn Starch or Casein Hydrolysate Drives Gut Microbiota-Related Bile Acid Metabolism To Stimulate Colonic Barrier Function – Yu Pi – mSystems

Plant, root and soil microbiome

Using Soil Bacterial Communities to Predict Physico-Chemical Variables and Soil Quality – Syrie M Hermans – Microbiome

Analysis of bacterial and archaeal communities associated with Fogo volcanic soils of different ages – Corinne Biderre-Petit – Fems Microbial Ecology

Water microbiome

Functional potential and assembly of microbes from sediments in a lake bay and adjoining river ecosystem for polycyclic aromatic hydrocarbon biodegradation – Zaisheng Yan – Environmental Microbiology

Functional foods

Effect of Probiotics on the Maintenance of Intestinal Homeostasis After Chemotherapy: Systematic Review and Meta-Analysis of Pre-Clinical Studies – W G Lima – Beneficial Microbes

Non microbiology picks

Racial Disparities in Knowledge, Attitudes and Practices Related to COVID-19 in the USA– Wilson M Alobuia – Journal of Public Health

Ozone Treatment for Elimination of Bacteria and SARS-CoV-2 for Medical Environments – Craig Westover – BioRxiv