Category Archives: Metagenomics & Bioinformatics

July 30, 2020

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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 27, 2020

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Greetings from Pittsburgh!

Saturday and Sunday’s digests were packed full of great articles, which means the week is off to a slower start than usual. We’ve got two environmentally focused preprints that I am super excited about, a paper demonstrating how microbiota can be dosed in order to help mice mitigate intestinal cancer and inflammation, and a paper focused on the eco-thermodynamics of methanogenic bioprocesses. Enjoy!

Animal experiments

Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis – Zhang et al. – Microbiome

Water and extremophile microbiome

Preprint: Distinct microbial communities along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents – Somee et al. – BioRxiv

Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses – Nobu et al. – Microbiome

Preprint: Freshwater monitoring by nanopore sequencing – Urban et al. – bioRxiv

July 25, 2020

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Good morning and happy Saturday y’all! Today’s digest is brief, but covers some fascinating papers including: small RNAs regulating gut microbe metabolism; epigenetics linking the early-life airway microbiota with allergic rhinitis; and the impact of gut microbial composition on vagal innervation. I’ve also included a non-microbiome pick discussing how to spot and resolve common statistical mistakes in research manuscripts. The authors of the article hope this will help improve robustness of scientific research. Happy reading!

Gut Microbiome
A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron. Ryan, D. et al. Nature Communications.

Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19. Zuo, T. et al. Gut.

High microbiota reactivity of adult human intestinal IgA requires somatic mutations. Kabbert, J. et al. Journal of Experimental Medicine.

A unified catalog of 204,938 reference genomes from the human gut microbiome. Almeida, A. et al. Nature Biotechnology.

Airway Microbiome
Epigenetic landscape links upper airway microbiota in infancy with allergic rhinitis at 6 years of age. Morin, A. et al. Journal of Allergy and Clinical Immunology.

Early-Life Microbiome
Butyrate producing colonic Clostridiales metabolise human milk oligosaccharides and cross feed on mucin via conserved pathways. Pichler, M.J. et al. Nature Communications.

Animal Experiments
Bile acids drive the newborn’s gut microbiota maturation. van Best, N. et al. Nature Communications.

Gut microbiota composition modulates inflammation and structure of the vagal afferent pathway. Kim, J.S. et al. Physiology & Behavior.

TNFα regulates intestinal organoids from mice with both defined and conventional microbiota. Sun, L. et al. International Journal of Biological Macromolecules.

Water Microbiome
Nutrient and microbial water quality of the upper Ganga River, India: identification of pollution sources. Bowed, M.J. et al. Environmental Monitoring and Assessment.

Plant, Root, and Soil Microbiome
Global warming shifts the composition of the abundant bacterial phyllosphere microbiota as indicated by a cultivation-dependent and -independent study of the grassland phyllosphere of a long-term warming field experiment. Aydogan, E.L. FEMS Microbiology and Ecology.

Non-Microbiome Pick
Science Forum: Ten common statistical mistakes to watch out for when writing or reviewing a manuscript. Makin, T.R. and Orban de Xivry, JJ. eLife.

July 19, 2020

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Hello from the Sonoran Desert! In today’s digest, you’ll find find a lot of very interesting papers! For those interested in host-phages interactions, there is an amazing work from Ping and collaborators looking at phage infections dynamics in migrating bacterial populations. Interestingly, the authors suggests that phages may be able to “hitchhike” with moving bacteria.

To continue with our viral readings, you’ll also find an interesting perspective paper from Kuprovic and collaborators. In this piece, the authors attempt to reconstruct the virome associated to LUCA (Last Universal Cellular Ancestor). Amazingly, their reconstruction shows that a remarkably complex virome would have been associated to LUCA, suggesting an extensive viral evolution antedating LUCA!

Finally, today’s non-microbiology pick is a book, looking at the fascinating Cuatro Ciénegas Basin, located in México, a site that is often described as a real outdoor laboratory for astrobiology. Indeed, the Basin site contains gypsum-rich soil analogous to the Gale Crater in Mars, and the ponds contains extremely oligotrophic waters, which can be used to model ancient oceans chemistry. You’ll explore along the chapters the history, ecology, microbiology and evolution of this amazing site, to unravel the mysteries of this site absolutely unique on the planet.

Have a great Sunday!

Human respiratory microbiome

Review: Insights gained into respiratory infection pathogenesis using lung tissue metabolomics –  Bernatchez and McCall –  PLOS Pathogens

Human gut microbiome

Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse workers: A metagenome-wide cross-sectional study –  Van Gompel et al. –  Environment International

Review: The influence of the gut microbiome on obesity –  Blanco – Journal of the American Association of Nurse Practitioners

Animal microbiome (for animals in the wild)

Comparative analysis of the gut microbiota of Apis cerana in Yunnan using high-throughput sequencing. –  Luo et al. –  Archives of Microbiology

Plant, root, and soil microbiome

Higher tree diversity increases soil microbial resistance to drought. –  Gillespie et al. –  Communications Biology

Effect of land uses on soil microbial community structures among different soil depths in northeastern China. –  Ji et al. –  European Journal of soil Biology

Structural variability and niche differentiation of the rhizosphere and endosphere fungal microbiome of Casuarina equisetifolia at different ages. –  Huang et al. –  Environmental Microbiology

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

Substrate regulation leads to differential responses of microbial ammonia-oxidizing communities to ocean warming. –  Zheng et al. –  Nature communications

Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel. –  Arsenieff et al.  –  The ISME Journal

Lake characteristics influence how methanogens in littoral sediments respond to terrestrial litter inputs. –  Yakimovich et al. –  The ISME Journal

Built environment (subways, indoor surfaces)

Heavy metal concentrations in Brazilian port areas and their relationships with microorganisms: can pollution in these areas change the microbial community? –  Del Busso Zampieri et al. –  Environmental Monitoring and Assessment

Food microbiology

Material conversion, microbial community composition and metabolic functional succession during green soybean hull composting. –  Zhang et al. –  Bioresource Technology

Phages and viruses

Hitchhiking, collapse, and contingency in phage infections of migrating bacterial populations. –  Ping et al. – The ISME Journal

Review: The LUCA and its complex virome. –  Krupovic et al. –  Nature Review Microbiology

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat. –  Jarett et al. –  ISME Journal

Bioinformatics

IDMIL: an alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data. –  Rahman and Rangwala –  Bioinformatics

My non-microbiology pick

Book: Astrobiology and Cuatro Ciénegas Basin as an Analog of Early Earth. –  Medina-Chávez et al. –  Cuatro Ciénegas Basin: An Endangered Hyperdiverse Oasis. Springer

July 15, 2020

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There are several notable entries in today’s digest. Registration is open for the European Learning Laboratory for the Life Sciences’ “Introducing Your Microbiome” virtual training course. The course is for European secondary school science teachers and is 5 weeks long. The 3rd Microbiome Movement will also be held this year, both virtually and in-person. Links are in the Events section.  

Today I’ve highlighted a bioinformatics paper on variant calling for cpn60 barcode sequencing and an early life paper on pre-term infant stem cell proliferation upregulated by microbial metabolites. While putting this digest together, I learned algae turns snow different colors! This is so cool to me that I’ve highlighted that paper as well. Finally, the News section includes an article for Smithsonian Magazine by Rob Dunn on quarantine’s effects on our microbial passengers.  

Happy reading!

Events

3rd Microbiome Movement – Animal Health & Nutrition Summit, taking place in North Carolina as well as digitally October 19-21, 2020.

European Learning Laboratory for the Life Sciences’ “Introducing Your Microbiome” November 2-December 7, 2020. Applications are due October 15 and the course is free.

Pregnancy and early life

Gut microbiota maturation during early human life induces enterocyte proliferation via microbial metabolites – Michael W. Dougherty – BMC Microbiology

Human gut microbiome

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

Microbiome of death

Characterizing the postmortem human bone microbiome from surface-decomposed remains – Alexandra L. Emmons – PloS One

Animal experiments

Saccharomyces cerevisiae fermentation products (SCFP) stabilize the ruminal microbiota of lactating dairy cows during periods of a depressed rumen pH – Hein M. Tun – BMC Veterinary Research

Animal microbiome

A Shift Pattern of Bacterial Communities Across the Life Stages of the Citrus Red Mite, Panonychus citri – Zhen-yu Zhang – Frontiers in Microbiology

Plant, root, and soil microbiome

Nitrogen enrichment stimulates wetland plant responses whereas salt amendments alter sediment microbial communities and biogeochemical responses – Mary Donato – PloS One

Bioavailable metal (loid) s and physicochemical features co-mediating microbial communities at combined metal (loid) pollution sites – Jiawen Wang – Chemosphere

Assessing the effects of tylosin fermentation dregs as soil amendment on macrolide antibiotic resistance genes and microbial communities: Incubation study – Bo Zhang – Journal of Environmental Science and Health, Part B

Book: Phytobiomes: Current Insights and Future Vistas – Manoj Kumar Solanki – Springer

Early changes in bacterial communities in wound tissues of Pinus massoniana after inoculation with Bursaphelenchus xylophilus – Jinyan Liu – Nematology

Preprint: Unexpected diversity of CPR bacteria and nanoarchaea in the rare biosphere of rhizosphere-associated grassland soil – Alexa M. Nicolas – bioRxiv

Preprint: A Meta-analysis of the known Global Distribution and Host Range of the Ralstonia Species Complex – Tiffany Lowe-Power – bioRxiv

Water, air, and extremophile microbiome

Lipid Biomarker Record of the Serpentinite-Hosted Ecosystem of the Samail Ophiolite, Oman and Implications for the Search for Biosignatures on Mars – Sharon A Newman – Astrobiology

Metabolic acclimation of anammox consortia to decreased temperature – Tangran Huo – Environment International

Complete Genome Sequences of Two Marine Biofilm Isolates, Leisingera sp. nov. Strains 201A and 204H, Novel Representatives of the Roseobacter Group – Giselle S. Cavalcanti – Microbiology Resource Announcements

Microbial interspecific interaction and nitrogen metabolism pathway for the treatment of municipal wastewater by iron carbon based constructed wetland – Xiao Huang – Bioresource Technology

Biogeographical distribution of dissimilatory nitrate reduction to ammonium (DNRA) bacteria in wetland ecosystems around the world – Huawei Pan – Journal of Soils and Sediments

Molecular diversity of the microbial community in coloured snow from the Fildes Peninsula (King George Island, Maritime Antarctica) – Wei Luo – Polar Biology

Novel arsenic hyper-resistant bacteria from an extreme environment, Crven Dol mine, Allchar, North Macedonia – Vladimir Bermanec – Journal of Hazardous Materials

Built environment

Ozone treatment in a wind tunnel for the reduction of airborne viruses in swine buildings – Jonathan M. Vyskocil – Aerosol Science and Technology

Food microbiology

Correlation between microbial communities and key flavors during post-fermentation of Pixian broad bean paste – Ping Liu – Food Research International

Additives affect the distribution of metabolic profile, microbial communities and antibiotic resistance genes in high-moisture sweet corn kernel silage – Zhe Wu – Bioresource Technology

Shifts in autochthonous microbial diversity and volatile metabolites during the fermentation of chili pepper (Capsicum frutescens L.) – Xinxing Xu – Food Chemistry

Proteomic characterization of extracellular vesicles produced by several wine yeast species – Ana Mencher – Microbioal Biotechnology

Book Chapter: Role of Microbes for Attaining Enhanced Food Crop Production – Pankaj Sharma – Microbial Biotechnology: Basic Research and Applications

Bioinformatics

Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling – Sarah J. Vancuren – PloS One

Techniques

Preprint: Visualization of giant virus particles using BONCAT labeling and STED microscopy – Monica Berjon-Otero – bioRxiv

Microbes in the News

Human Microbiome: 39 trillion microbes and bacteria that call us home – Mun-Keat Looi – Science Focus

What Quarantine is Doing to Your Body’s Wondrous World of Bacteria – Rob Dunn – Smithsonian Magazine

July 13, 2020

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Greetings from Pittsburgh, PA!

Included is a wide range of microbial ecology articles focused on everything from the human microbiome to soil microbial fuel cells. I want to give a special highlight to the article about how the indoor microbial community changes in response to bed bug infestations. This study incorporates a few of my favorite disciplines including entomology, public health, the built environment, as well as microbiology. If you’re interested in learning more about bed bugs, I’ll also recommend one my favorite reads from a few years ago: Infested: How the bed bug infiltrated our bedrooms and took over the world by Brooke Borel.

Events and jobs

In my last microbiome digest, I gave a special plug for the National Summer Undergraduate Research Project (NSURP). NSURP is a community-driven initiative to create rewarding remote summer research opportunities for BIPOC undergraduate students in the microbial sciences. They have already paired over 140 students with summer research opportunities, but they still need mentors for remaining student applicants. Please apply and share widely!

General microbiome

The beta-diversity of Siganus fuscescens-associated microbial communities from different habitats increases with body weight – Wu et al. – Frontiers in Microbiology

Human gut microbiome

Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut – Chng et al. – Nature Ecology & Evolution

The gut microbiome during acute lifestyle transition – Devkota – Nature Medicine

Review: Challenges and emerging systems biology approaches to discover how the human gut microbiome impact host physiology – Wian and Ho – Biophysical Reviews

Animal experiments

The gut and feed residue microbiota changing during the rearing of Hermetia illucens larvae – Cifuentes et al. – Antonie van Leeuwenhoek

Animal microbiome

Effect of introduced parasites on the survival and microbiota of nestling cactus finches (Geospiza scandens) in the Galápagos Islands – Addesso et al. – Journal of Ornithology

Direct comparison of fecal and gut microbiota in the Blue Mussel (Mytilus edulis) discourages fecal sampling as a proxy for resident gut community – Griffin et al. – Microbial Ecology

Plant, root, and soil microbiome

Variable microbial communities in the non-hydrothermal sediments of the Mid-Okinawa trough – Cao et al. – Geomicrobiology Journal

Review: Microbial communities from arid environments on a global scale. A systematic review – Vásquez-Dean et al. – Biological Research

Unravelling metabolism and microbial community of a phytobed co-planted with Typha angustifolia and Ipomoea aquatica for biodegradation of doxylamine from wastewater – Xiong et al. – Journal of Hazardous Materials

Built environment

Bed bugs shape the indoor microbial community composition of infested homes – Kakumanu et al. – Science of the Total Environment

Effect of sono-thermal pre-treatment over methane production, specific activities and the microbial community of sludge anaerobic digesters – Neumann et al. – Waste and Biomass Valorization

Effects of anode materials on the performance and anode microbial community of soil microbial fuel cell – Yu et al. – Journal of Hazardous Material

Techniques

Review: Targeted microbiome depletion – Du Toit – Nature Reviews Microbiology

July 10, 2020

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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 8, 2020

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Good morning! Today’s digest includes a broad selection of interesting research. Particular highlights include a study in rats that found microbiota transplantation attenuated neuroinflammation, a human study on the dramatic microbiome effects of dietary glycans, and a new technique for using drones to collect dolphin microbiome samples.

Pregnancy and early life

History of breastfeeding but not mode of delivery shapes the gut microbiome in childhood, Camille C. Cioffi et al., PLOS ONE

Preprint: Gut microbiota and fecal short-chain fatty acids are not associated with bone mass in healthy Chinese children: a cross-sectional study, Fengyan Chen et al., Research Square

Impact of Long-Term and Low-Dose Antibiotic Prophylaxis on Gut Microbiota in Children, Yuko Akagawa et al., The Journal of Urology

Human gut microbiome

Microbiome and health implications for ethnic minorities after enforced lifestyle changes, David M. Keohane et al., Nature Medicine

Preprint: Metaproteomics reveals potential signatures of disease-specific alterations in the gut microbial proteolytic events in inflammatory bowel disease, Zhixiang Yan et al., Research Square

High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans, Richard Creswell et al., Genome Medicine

Preprint: High-throughput cultivation of stable, diverse, fecal-derived microbial communities to model the intestinal microbiota, Andres Aranda-Diaz et al., bioRxiv

Preprint: pH-dependent spontaneous hydrolysis rather than gut bacterial metabolism reduces levels of the ADHD treatment, Methylphenidate, Julia Aresti et al., bioRxiv

Animal experiments

The gut microbiota attenuate neuroinflammation in manganese exposure by inhibiting cerebral NLRP3 inflammasome, Wang and Yang et al., Biomedicine & Pharmacotherapy

Magnetic fields modulate metabolism and gut microbiome in correlation with Pgc‐1α expression: Follow‐up to an in vitro magnetic mitohormetic study, Yee Kit Tai et al., The FASEB Journal

Preprint: Multi-omics analysis of aspirin treatment response in mice provide molecular insights and targets linked to liver fibrosis regression, Adil Bhat et al., bioRxiv

Animal microbiome

Limited influence of the microbiome on the transcriptional profile of female Aedes aegypti mosquitoes, Josephine Hyde et al., Scientific Reports

The gut bacterial microbiota of sea turtles differs between geographically distinct populations, T. Franciscus Scheelings et al., Endangered Species Research

Bioinformatics

Sparse reduced-rank regression for integrating omics data, Hilafu, Safo and Haine, BMC Bioinformatics

Techniques

An ecological framework to understand the efficacy of fecal microbiota transplantation, Yandong Xiao et al., Nature Communications

The use of Unmanned Aerial Vehicles (UAVs) to sample the blow microbiome of small cetaceans, Cinzia Centelleghe et al., PLOS ONE

July 7, 2020

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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

July 4, 2020

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Greetings from Santiago, Chile! Today in this Digest, we have studies about the influence of alcohol use disorder on the microbiota, several papers about the influence of different compounds (from allicin to DAV132, a colon-targeted antibiotic adsorbent) on the microbiota. Today we have several papers about different models of plant- or soil- associated microbiomes, and a couple of papers from studies with SIV infection models. Have a nice weekend!

Human and General Microbiome

Longitudinal gut microbiome changes in alcohol use disorder are influenced by abstinence and drinking quantity – Nancy Ames et al., – Gut Microbes

Comparative evaluation of peptidome and microbiota in different types of saliva samples – Ce Zhu et al., – Annals of Translational Medicine

Preprint: Microbial control over host diet selection – Brian K Trevelline and Kevin D Kohl – BioRxiv

Functional Compounds and the Microbiome

Hemolysin BL from novel Bacillus toyonensis BV-17 induces antitumor activity both in vitro and in vivo – Jiajia Chen et al., – Gut Microbes

Modeling the effect of DAV132, a novel colon-targeted adsorbent, on fecal concentrations of moxifloxacin and gut microbiota diversity in healthy volunteers – Jinju Guk et al., – Clinical Pharmacology and Therapeutics

Allicin-induced host-gut microbe interactions improves energy homeostasis – Chuanhai Zhang et al., – The FASEB Journal

Evidence of Microbiome-Drug Interactions between the Antimalarial Lumefantrine and Gut Microbiota in Mice – Matthew M. Ippolito et al., – The American Society of Tropical Medicine and Hygiene

Contrasting effects of viscous and particulate fibers on colonic fermentation in vitro and in vivo, and their impact on intestinal water studied by MRI in a randomized trial – David Gunn et al., – The American Journal of Clinical Nutrition

Animal Microbiome / Animal Models

A theoretic approach to the mode of gut microbiome translocation in SIV-infected Asian macaques – Wendy Li and Zhanshan (Sam) Ma – FEMS Microbiology Ecology

Impact of Initial Feeding and Molting on Tachypleus tridentatus Gut Microbiota – Fengze Miao et al., – Current Microbiology 

Osmotic stress induces gut microbiota community shift in fish – Keng Po Lai et al., – Environmental Microbiology

The Gut-Eye Axis: Lessons Learned from Murine Models – Jason L. Floyd & Maria B. Grant – Ophthalmology and Therapy 

The colonic mucosa-associated microbiome in SIV infection: shift towards Bacteroidetes coincides with mucosal CD4+ T cell depletion and enterocyte damage – Kristina Allers et al., – Scientific Reports  

Plant or Soil Microbiomes

Re-Analysis of 16S Amplicon Sequencing Data Reveals Soil Microbial Population Shifts in Rice Fields under Drought Condition – Seok-Won Jang et al, – Rice 

Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations – Ryan S. McClure et al., – Scientific Reports 

Potential microbial bioindicators of phosphorus mining in a temperate deciduous forest – Laura M. Mason et al.,– Journal of Applied Microbiology

Phylogenetic signals and predictability in plant-soil feedbacks – Elizabeth M. Wandrag et al., – New Phytologist

Genomics / Bioinformatics

The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites – Feifei Xu et al., – Microbial Genomics 

LEMMI: A continuous benchmarking platform for metagenomics classifiers – Mathieu Seppey et al., – Genome Research

Other papers

Preprint: Metagenome-assembled genomes from Monte Cristo Cave (Diamantina, Brazil) reveal prokaryotic lineages as functional models for life on Mars – Amanda G Bendia et al., – BioRxiv 

Preprint: Exploring metal resistance genes and mechanisms in copper enriched metal ore metagenome – Esmaeil Forouzan Sr. et al., – BioRxiv

SARS-CoV-2 Preprints

Preprint: Alpha-1 antitrypsin inhibits SARS-CoV-2 infection – Lukas Wettstein et al., – BioRxiv