Category Archives: Human reproductive or urinary

October 30, 2018

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Hello everyone! Today’s digest includes gut microbiome inheritance in Drosophila, the influence of diet on dairy calf microbiomes, and axenic mosquitoes. Have a great day!

Pregnancy and early life

The gut microbiota in infants of obese mothers increases inflammation and susceptibility to NAFLD – Soderborg – Nature Communications

Neonatal gut and respiratory microbiota: coordinated development through time and space – Grier – Microbiome

Human urinary microbiome

Urinary Microbiome Associated with Chronic Allograft Dysfunction in Kidney Transplant Recipients – Wu – Clinical Transplantation

Human gut microbiome

Review: Antibiotics as both friends and foes of the human gut microbiome: The microbial community approach – Nogueira – Drug Development Research

Animal experiments

Microbial structure and function in infant and juvenile rhesus macaques are primarily affected by age, not vaccination status – Hasegawa – Scientific Reports

The gut microbiome participates in transgenerational inheritance of low temperature responses in Drosophila melanogaster – Zare – FEBS Letters

The impact of exercise training and resveratrol supplementation on gut microbiota composition in high-fat diet fed mice – Brandt – Physiological Reports

Effect of fecal microbiota transplantation route of administration on gut colonization and host response in preterm pigs – Brunse – ISME

Animal microbiome

Bacterial community structure and succession in nests of two megachilid bee genera – Voulgari-Kokota – FEMS Microbiology Ecology

Gut microbial divergence between two populations of the hadal amphipod Hirondellea gigas – Zhang – Applied and Environmental Microbiology

Diet influences early microbiota development in dairy calves without long-term impacts on milk production – Dill-McFarland – Applied and Environmental Microbiology

Generation of axenic Aedes aegypti demonstrate live bacteria are not required for mosquito development – Correa – Nature Communications

Plant, root, and soil microbiome

Review: Influence of Light on Plant-Phyllosphere Interaction – Carvalho – Frontiers in Plant Science

Deciphering the bacterial composition in the rhizosphere of Baphicacanthus cusia (NeeS) Bremek – Zeng – Scientific Reports

Changes in Metal Availability and Improvements in Microbial Properties After Phytoextraction of a Cd, Zn and Pb Contaminated Soil – Yang – Bulletin of Environmental Contamination and Toxicology

Legacy of land use history determines reprogramming of plant physiology by soil microbiome – Li – ISME

Adaptation of soil microbial growth to temperature: using a tropical elevation gradient to predict future changes – Nottingham – Global Change Biology

Soil pH rather than elevation determines bacterial phylogenetic community assembly on Mt. Norikura, Japan – Cho – FEMS Microbiology Ecology

Foliar fungal endophyte communities are structured by environment but not host ecotype in Panicum virgatum (switchgrass) – Whitaker – Ecology

Built environment

Mapping anaerobic sludge bed community adaptations to manure supernatant in biogas reactors – Synnøve Røstad Nordgård – Scientific Reports

Microbial activity response to hydrogen injection in thermophilic anaerobic digesters revealed by genome-centric metatranscriptomics – Fontana – Microbiome

October 27, 2018

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Have a good weekend!

Today, in this Digest we have a good amount of articles, including: a study showing the importance of the gut microbiota in the development of thrombosis; the effect of a probiotic on patients with coronary artery disease; a study about vaginal microbiota and menopause; a study gaining insights about the natural microbiota transmission;  associations between microbiota and exercise, and more!

 

Gut Microbiome

Microbial Transplantation With Human Gut Commensals Containing CutC Is Sufficient to Transmit Enhanced Platelet Reactivity and Thrombosis Potential – Sarah M. Skye  – Circulation Research. Comment about this paper in the Editorial: Microbiota-Derived Trimethylamine, The Missing Jigsaw Piece in Thrombosis? – Klytaimnistra Kiouptsi

Gut microbiome and type 2 diabetes: where we are and where to go? – Sapna Sharma – The Journal of Nutritional Biochemistry

The gut microbiome of Mexican children affected by obesity – Otoniel Maya-Lucas – Anaerobe

Endurance exercise and gut microbiota: A review – Núria Mach – Journal of Sport and Health Science

Fecal microbiota transplantation confers beneficial metabolic effects of diet and exercise on diet-induced obese mice – Zi-Lun Lai – Scientific Reports

Trimethylamine N-Oxide and Risk of Cardiovascular Disease and Mortality – Chanavuth Kanitsoraphan – Current Nutrition Reports

A comprehensive analysis of the faecal microbiome and metabolome of Strongyloides stercoralis infected volunteers from a non-endemic area – Timothy P. Jenkins – Scientific Reports

Clostridioides difficile uses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea – Eric J. Battaglioli – Science Translational Medicine

Opportunistic bacteria confer the ability to ferment prebiotic starch in the adult cystic fibrosis gut – Yanan Wang – Gut Microbes

Towards an Individualized Nutrition Treatment: Role of the Gastrointestinal Microbiome in the Interplay Between Diet and Obesity – Solveig A. Adalsteinsdottir – Current Obesity Reports

Increasing Dietary Fiber Intake Is Associated with a Distinct Esophageal Microbiome – Yael R. Nobel – Clinical and Translational Gastroenterology

Clostridial Butyrate Biosynthesis Enzymes Are Significantly Depleted in the Gut Microbiota of Nonobese Diabetic Mice – Alessandro Tanca – mSphere

Modelling the role of microbial p-cresol in colorectal genotoxicity – Eiman Abdulla Al Hinai – Gut Microbes

Diet and Psychosis: A Scoping Review – M. Aucoin – Neuropsychobiology

Minireview: Inflammation and Gut-Brain Axis During Type 2 Diabetes: Focus on the Crosstalk Between Intestinal Immune Cells and Enteric Nervous System – Arnaud Bessac – Frontiers in Neuroscience

Effects of water decontamination methods and bedding material on the gut microbiota – Willie A. Bidot – PLOS One

Timing for the second fecal microbiota transplantation to maintain the long-term benefit from the first treatment for Crohn’s disease – Pan Li – Applied Microbiology and Biotechnology

Gut microbiome disruption altered the biotransformation and liver toxicity of arsenic in mice – Liang Chi – Archives of Toxicology

 

Early Life Microbiome

Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort – Maggie A. Stanislawski – mBio

Differences in the fecal microbiota of neonates born at home or in the hospital – Joan L. Combellick – Scientific Reports

Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure – Joann Romano-Keeler – PLOS One

 

Oral, Nasal and Respiratory Tract Microbiome

Keystone Species in Pregnancy Gingivitis: A Snapshot of Oral Microbiome During Pregnancy and Postpartum Period – Preethi Balan – Frontiers in Microbiology

The Oral Microbiota Is Modified by Systemic Diseases – D.T. Graves – Journal of Dental Research

Prospective Study of Oral Microbiome and Colorectal Cancer Risk in Low-income and African American Populations – Yaohua Yang – International Journal of Cancer

Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes – Joshua P. Earl – Microbiome

The effect of maxillary sinus antrostomy size on the sinus microbiome – Alexander S. Kim – International Forum of Allergy & Rhinology

Microbiome dataset from the upper respiratory tract of patients living with HIV, HIV/TB and TB from Myanmar – Kyaw Soe Htun – Data in Brief

Variations of the lung microbiome and immune response in mechanically ventilated surgical patients – Ryan M. Huebinger – PLOS One

Root Microbiota in Primary and Secondary Apical Periodontitis – Serge Bouillaguet – Frontiers in Microbiology

 

Reproductive / Urinary Tract Microbiome and Health

Association between the vaginal microbiota, menopause status, and signs of vulvovaginal atrophy – Rebecca M. Brotman – Menopause

Association of Pelvic Inflammatory Disease with Risk of Endometriosis: A Nationwide Cohort Study Involving 141,460 Individuals – Fei-Wu Tai – Journal of Clinical Medicine

 

Beneficial Microbes and Compounds

Lactobacillus plantarum 299v Supplementation Improves Vascular Endothelial Function and Reduces Inflammatory Biomarkers in Men With Stable Coronary Artery Disease – Mobin Malik – Circulation Research. About this article: The Microbiome and Endothelial Function – Jhansi L. Leslie 

Probiotics for gastrointestinal and liver diseases: an updated review of the published literature – Francis E. Dailey – Endocrine, Metabolic & Immune Disorders – Drug Targets

Review: Immunological Tolerance and Function: Associations Between Intestinal Bacteria, Probiotics, Prebiotics, and Phages – Luis Vitetta – Frontiers in Immunology

Protective Effect of Pediococcus pentosaceus LI05 Against Clostridium difficile Infection in a Mouse Model – Qiaomai Xu – Frontiers in Microbiology

Mixture of Two Lactobacillus plantarum Strains Modulates the Gut Microbiota Structure and Regulatory T Cell Response in Diet-Induced Obese Mice – Jieun Lee – Molecular Nutrition & Food Research

Microbiota stability in healthy individuals after single-dose lactulose challenge-A randomized controlled study – Sandra Y. Wotzka – PLOS One

Review: Interactions of Surface Exopolysaccharides From Bifidobacterium and Lactobacillus Within the Intestinal Environment – Nuria Castro-Bravo – Frontiers in Microbiology

Rapid differentiation of Lactobacillus species via metabolic profiling – Kundi Yang – Journal of Microbiological Methods

Combining probiotics and an angiotensin-II type 1 receptor blocker has beneficial effects on hepatic fibrogenesis in a rat model of nonalcoholic steatohepatitis – Yasuhiko Sawada – Hepatology Research

Antidepressant Effects of Rosemary Extracts Associate With Anti-inflammatory Effect and Rebalance of Gut Microbiota – Ying Guo – Frontiers in Pharmacology

Association of dietary fibre intake and gut microbiota in adults – Daniel Lin – British Journal of Nutrition

Effect of prebiotic and probiotic supplementation on neurodevelopment in preterm very low birth weight infants: findings from a meta-analysis – Ravi Prakash Upadhyay – Pediatric Research

Potential of Maintaining a Healthy Vaginal Environment by Two Lactobacillus Strains Isolated from Cocoa Fermentation – Ana Clara Correia Melgaço – BioMed Research International

Viability of microencapsulated Akkermansia muciniphila and Lactobacillus plantarum during freeze-drying, storage and in vitro simulated upper gastrointestinal tract passage – Martín Sebastián Marcial-Coba – Food & Function

Single probiotic supplement suppresses colitis-associated colorectal tumourigenesis by modulating inflammatory development and microbial homeostasis – Jingjing Rong – Journal of Gastroenterology and Hepatology

Exploring Effects of Chitosan Oligosaccharides on Mice Gut Microbiota in in vitro Fermentation and Animal Model – Chen Zhang – Frontiers in Microbiology

Microbiome Analysis of Biofilms of Silver Nanoparticle-Dispersed Silane-Based Coated Carbon Steel Using a Next-Generation Sequencing Technique – Akiko Ogawa – Antibiotics

Formation of silver nanoparticles by human gut microbiota – Naiyi Yin – Science of The Total Environment

 

Skin Microbiome

Effect of an Emollient on the Mycobiome of Atopic Dermatitis Patients – Jyotsna Chandra – Journal of Drugs in Dermatology

 

General Microbiome

Transmission modes of the mammalian gut microbiota – Andrew H. Moeller – Science

Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites – Janko Tackmann – Microbiome

Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing – Morgane Mailhe – BMC Microbiology

gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data – W. Shi – Nucleic Acid Research

Antibiotics and autoimmune and allergy diseases: Causative factor or treatment? – Anna Strzępa – International Immunopharmacology

Pearls: Bacteriophages shift the focus of the mammalian microbiota – Breck A. Duerkop – PLOS Pathogens

 

Environmental Microbiome

Bleaching-Associated Changes in the Microbiome of Large Benthic Foraminifera of the Great Barrier Reef, Australia – Martina Prazeres – Frontiers in Microbiology

October 23, 2018

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Here comes today’s Microbiome Digest featuring the recent articles on microbial methane oxidizers, sulfidic waters, PM exposure effect on airway microbiome, dysbiotic state of spring fever, diets targeting microbiome and be a cure, peri-implantitis, effect of age and inflammation on mice microbiome, diet effect on monkeys microbiome, fecal microbial transplant in UC patients, cervical microbiome, functional repertoire of ETEC and Bifidobacterium, bile duct inflammation causing microbes, role of probiotics. HAPPY READING.

EVENTS, JOBS, SCHOLARSHIPS:

Commonwealth PhD Scholarships – Study at UK University

ENVIRONMENTAL MICROBIOME:

Regulation of coastal methane sinks by a structured gradient of microbial methane oxidizers – He Z – Environ Pollut

Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters – Deja-Sikora E – Microb Ecol

HUMAN RESPIRATORY MICROBIOME:

Airway microbiome is associated with respiratory functions and responses to ambient particulate matter exposure – Wang L – Ecotoxicol Environ Saf

ORAL MICROBIOME:

Oral microbiota dysbiosis and its association with Henoch-Schönlein Purpura in children – Chen B – Int Immunopharmacol

The Severity of Human Peri-Implantitis Lesions Correlates with the Level of Submucosal Microbial Dysbiosis – Kröger A – J Clin Periodontol

Increased transferrin saturation is associated with subgingival microbiota dysbiosis and severe periodontitis in genetic haemochromatosis – Boyer E – Sci Rep

Effects of antimicrobial peptide GH12 on the cariogenic properties and composition of a cariogenic multispecies biofilm – Jiang W – Appl Environ Microbiol
GUT MICROBIOME:

Review: Natural polysaccharides exhibit anti-tumor activity by targeting gut microbiota – Liu L – Int J Biol Macromol

Polysaccharides from Laminaria japonica alleviated metabolic syndrome in BALB/c mice by normalizing the gut microbiota – Duan M – Int J Biol Macromol.

Gut microbiota translocation promotes autoimmune cholangitis – Ma HD – J Autoimmun

Competitive lottery-based assembly of selected clades in the human gut microbiome – Verster AJ- Microbiome

Mini-Review : Leaky Gut, Leaky Brain? – Obrenovich MEM – Microorganisms

REPRODUCTIVE MICROBIOME:

Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study – Arokiyaraj S –
Sci Rep

ANIMAL MODEL MICROBIOME:

Long-term intake of Lactobacillus paracasei KW3110 prevents age-related chronic inflammation and retinal cell loss in physiologically aged mice – Morita Y – Aging

Targeted Diet Modification Reduces Multiple Sclerosis-like Disease in Adult Marmoset Monkeys from an Outbred Colony – Kap YS – J Immuno

FUNCTIONAL REPERTOIRE INSIGHTS:

Cell surface polysaccharides of Bifidobacterium bifidum induce the generation of Foxp3+ regulatory T cells – Verma R – Sci Immunol.

De-O-Acetylation of mucin-derived sialic acids by recombinant NanS-p esterases of Escherichia coli O157:H7 strain EDL933 – Feuerbaum S – Int J Med Microbiol.

PLANT MICROBIOME:

The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales – Li HY- Microbiome

METHODS:

Protocol for faecal microbiota transplantation in ulcerative colitis (FMTUC): a randomised feasibility study – Jitsumura M – BMJ Open

PROBIOTICS:

Probiotics in Autoimmune and Inflammatory Disorders – Liu Y – Nutrients

NON-MICROBIOME PICK:

Preprint: Segregational drift and the interplay between plasmid copy number and evolvability – Judith Ilhan- Biorxiv

October 19, 2018

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Today’s Digest provides much food for thought. Highlights include how to identify keystone species, a seminal review on the long-term and short-term effects of C-section on mom and child’s health, and a new de novo assembler for short metagenomic reads.

General microbiology

Antibiotic export by efflux pumps affects growth of neighboring bacteria – Xi Wen et al. – Scientific Reports

Proteomic analysis of four Clostridium botulinum strains identifies proteins that link biological responses to proteomic signatures – Brooke L. Deatherage Kaiser et al. – PLoS One

Biodiversity‐function relationships in methanogenic communities – Pawel Sierocinski et al. – Molecular Ecology

Solubilization and degradation of polychlorinated biphenyls (PCBs) by naturally occurring facultative anaerobic bacteria – Gathanayana Pathiraja et al. – Science of the Total Environment

An improved neutral community model for temporal observations in microbial communities – Li Jie & Shen Xuzhu – Ecological Modelling

** Identifying Keystone Species In The Microbial Community Based On Cross-sectional Data – Min Li et al. – Current Gene Therapy

Does quorum sensing interference affect the fitness of bacterial pathogens in the real world? – Yiying Liu et al. – Environmental Microbiology

Pregnancy and early life

Microbiota and Derived Parameters in Fecal Samples of Infants with Non-IgE Cow’s Milk Protein Allergy under a Restricted Diet – María Díaz et al. – Nutrients

** Review: Short-term and long-term effects of caesarean section on the health of women and children – Jane Sandall et al. – Lancet

Human skin microbiome

The Skin Microbiota in Patients Hospitalized for Cellulitis and Association With Outcome – Duncan R Cranendonk et al. – Clinical Infectious Diseases

Human multi-site microbiome

Continuous Antibiotic Prophylaxis in Pediatric Urology – Douglas W.Storm et al. – Urologic Clinics of North America

Human gut microbiome

Impact of antibiotic use on survival in patients with advanced cancers treated on immune checkpoint inhibitor phase I clinical trials – S Sen et al. – Journal of Experimental Medicine

Review: Visceral pain: gut microbiota, a new hope? – Matteo M Pusceddu & Melanie G Gareau – Journal of Biomedical Science

Review: Vulnerability of long-term care facility residents to Clostridium difficile infection due to microbiome disruptions – Beth Burgwyn Fuchs et al. – Future Microbiology

Fecal Microbiota Transplant for Recurrent Clostridium Difficile Infection in Pediatric Inflammatory Bowel Disease – Cho, Stanley et al. – Journal of Pediatric Gastroenterology and Nutrition

Transcriptome meta-analysis identifies immune signature comprising of RNA binding proteins in ulcerative colitis patients – Saima Naz et al. – Cellular Immunology

Alterations of Gut Microbiome in the Patients With Severe Fever With Thrombocytopenia Syndrome – Honghai Xu et al. – Frontiers in Microbiology

Review: Role of Gut Microbiota in the Development and Treatment of Colorectal Cancer – LIN C. et al. – Digestion

Human gut-microbiome-brain axis

A primer on investigating the role of the microbiome in brain and cognitive development – Caroline Kelsey et al. – Developmental Psychology

Animal experiments

Grape polyphenols reduce gut-localized reactive oxygen species associated with the development of metabolic syndrome in mice – Peter Kuhn et al. – PLoS One

Host developmental toxicity of BPA and BPA alternatives is inversely related to microbiota disruption in zebrafish – Tara R Catron et al. – Toxicological Sciences

Liver Injury, Endotoxemia, and Their Relationship to Intestinal Microbiota Composition in Alcohol-Preferring Rats – Brunella Posteraro et al. – Alcoholism Clinical & Experimental Research

Liver tumorigenesis is promoted by a high saturated-fat diet specifically in male mice and is associated with hepatic expression of the proto-oncogene Agap2 and enrichment of the intestinal microbiome with Coprococcus – Kim B Pedersen et al. – Carcinogenesis

Animal microbiome

Host species, pathogens and disease associated with divergent nasal microbial communities in tortoises – Chava L. Weitzman et al. – Royal Society Open Science

Review: Understanding the Milk Microbiota – Stephanie A.Metzger et al. – Veterinary Clinics of North America: Food Animal Practice

Evolution of the nasopharyngeal bacterial microbiota of beef calves from spring processing to 40 days after feedlot arrival – Christopher McMullen et al. – Veterinary Microbiology

Plant, root and soil microbiome

Review: The impact of microbes in the orchestration of plants’ resistance to biotic stress: a disease management approach – Matthew Chekwube Enebe & Olubukola Oluranti Babalola – pplied Microbiology and Biotechnology

Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts – Xuepeng Sun et al. New Phytologist

Facilitation promotes invasions in plant-associated microbial communities – Wei, Zhong et al. – Ecology Letters

Water and extremophile microbiome

Temperature Controls Crystalline Iron Oxide Utilization by Microbial Communities in Methanic Ferruginous Marine Sediment Incubations – David A. Aromokeye et al. – Frontiers in Microbiology

Bacterial community changes in a glacial-fed Tibetan lake are correlated with glacial melting – Keshao Liu et al. – Science of The Total Environment

Food microbiology

Review: Fermentation trip: amazing microbes, amazing metabolisms – Rong Feng et al. – Annals of Microbiology

Phages and viruses

Complete Genome Sequence of the Model Halovirus PhiH1 (ΦH1) – Mike Dyall-Smith et al. – Genes

Technology

Rapid identification of pathogens from positive blood culture bottles with the MinION nanopore sequencer – Sae Ashikawa et al. – Journal of Medical Microbiology

The use of broad-range bacterial PCR in the diagnosis of infectious diseases: a prospective cohort study – Jan Tkadlec et al. – Clinical Microbiology and Infection

Bioinformatics

BlasterJS: A novel interactive JavaScript visualisation component for BLAST alignment results – Aitor Blanco-Míguez et al. – PLoS One

Review: Integrating–omics data into genome-scale metabolic network models: principles and challenges – Charlotte Ramon et al. – Essays in Biochemistry

** High-quality genome sequences of uncultured microbes by assembly of read clouds – Alex Bishara et al. – Nature Biotechnology

Microbes in the news

Cecilia Jonsson Serenades Sewage Bacteria – Sofia Bergmann – Berlin Art Link

October 15, 2018

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In today’s Digest, you’ll find a method for museum collections to identify helminth communities in small mammals, new results in the urinary and vaginal microbiome, the effects of HIV PrEP and broccoli on the gut microbiome, and fungal communities associated with plant roots. Happy reading!

General microbiome
Review: Probiotics importance and their immunomodulatory properties. – Bahman Yousefi – Journal of Cellular Physiology

Review: An insight into gut microbiota and its functionalities. – Atanu Adak – Cellular and Molecular Life Sciences

Gut-brain axis
Review: A primer on investigating the role of the microbiome in brain and cognitive development. – Caroline Kelsey – Developmental Psychobiology

Human vaginal microbiome
Preprint: Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: Implications for in vivo dominance of the vaginal microbiota – Charlotte van der Veer – bioRxiv

Human urinary microbiome
Community profiling of the urinary microbiota: considerations for low-biomass samples. – Lisa Karstens – Nature Reviews Urology

Human gut microbiome
Daily HIV pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate-emtricitabine reduced Streptococcus and increased Erysipelotrichaceae in rectal microbiota. – Michael P. Dubé – Scientific Reports

Broccoli consumption affects the human gastrointestinal microbiota – Jennifer L. Kaczmarek – The Journal of Nutritional Biochemistry

Intestinal dysbiosis in Inflammatory Bowel Disease associated with primary immunodeficiency. – Harry Sokol – Journal of Allergy and Clinical Immunology

Chronic kidney disease after 5/6 nephrectomy disturbs the intestinal microbiota and alters intestinal motility. – Kazuhiro Nishiyama – Journal of Cellular Physiology

Animal microbiome
Museum metabarcoding: a novel method revealing gut helminth communities of small mammals across space and time. – Stephen E. Greiman – International Journal for Parasitology

Showcasing the role of seawater in bacteria recruitment and microbiome stability in sponges. – Marta Turon – Scientific Reports

Animal experiments
Microcapsule of sweet orange essential oil changes gut microbiota in diet-induced obese rats. – Dahu Li – Biochemical and Biophysical Research Communications

Changes in ruminal and reticular pH and bacterial communities in Holstein cattle fed a high-grain diet. – Yo-Han Kim – BMC Veterinary Research

Plant, root, and soil microbiome
Dibutyl phthalate contamination remolded the fungal community in agro-environmental system – Xiao Kong – Chemosphere

Plant‐mediated effects of soil phosphorus on the root‐associated fungal microbiota in Arabidopsis thaliana – Izabela Fabiańska – New Phytologist

Water and extremophile microbiome
Prokaryotic Diversity and Distribution in Different Habitats of an Alpine Rock Glacier-Pond System. – I. Mania – Microbial Ecology

Preprint: Response of extremophile microbiome to a rare rainfall reveals a two-step adaptation mechanism – Gherman Uritskiy – bioRxiv

Bioinformatics
Preprint: Nomenclature Errors in Public 16S rRNA Gene Reference Databases – Kyle James Lesack – bioRxiv

October 9, 2018

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Pregnancy and early life

Gut Microbiota and Body Weight in School‐Aged Children: The KOALA Birth Cohort Study – Catherine A. Mbakwa – Obesity

Multi-site human microbiome

Grow With the Challenge – Microbial Effects on Epithelial Proliferation, Carcinogenesis, and Cancer Therapy – Jakob von Frieling – Frontiers in Microbiology

Human respiratory microbiome

Microbiome dataset from the upper respiratory tract of patients living with HIV, HIV/TB and TB from Myanmar – Kyaw SoeHtuna – Data in Brief

Human skin microbiome

The microbiome of the “sterile” pustules in palmoplantar pustulosis – Kana Masuda‐Kuroki – Experimental Dermatology

Human vaginal microbiome

Evaluation of patient- versus provider-collected vaginal swabs for microbiome analysis during pregnancy – Kristine M. Wylie – BMC Research Notes

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Animal experiments

Protective effects of a triple-fermented barley extract (FBe) against HCl/EtOH-induced gastric mucosa damage in mice – Jong‐Min Lim – Food Science & Nutrition

Guarana (Paullinia cupana Mart.) alters gut microbiota and modulates redox status, partially via caffeine in Wistar rats – Alexandre Kleber Silveira – Phytotherapy Research

Gut microbiota–dependent modulation of innate immunity and lymph node remodeling affects cardiac allograft outcomes – Jonathan S. Bromberg – JCI Insight

Prokaryotic communities of Indo-Pacific giant barrel sponges are more strongly influenced by geography than host phylogeny – T Swierts – FEMS Microbiology Ecology

In vitro experiments

A Simple In Vitro Gut Model for Studying the Interaction between Escherichia coli and the Intestinal Commensal Microbiota in Cecal Mucus – Matthew E Mokszycki – Applied and Environmental Microbiology

Animal microbiome

Tissue-specific immune responses to Vibrio sp. infection in mussels (Perna canaliculus): A metabolomics approach – Thao V. Nguyen – Aquaculture

Conserved microbiota among young Heliconius butterfly species – Bas van Schooten – Peer J

Microbial community composition of nest-carton and adjoining soil of the ant Lasius fuliginosus and the role of host secretions in structuring microbial communities – Pina Brinker – Fungal Ecology

Comparative metagenomics of the gut microbiota in wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea) – Wen Wang – Microbiology Open

Microbiome and Blood Analyte Differences Point to Community and Metabolic Signatures in Lean and Obese Horses – Amy S. Biddle – Frontiers in Veterinary Science

Plant, root, and soil microbiome

Determinants of Deadwood-Inhabiting Fungal Communities in Temperate Forests: Molecular Evidence From a Large Scale Deadwood Decomposition Experiment – Witoon Purahong –

Induction of defense mechanisms involved in disease resistance of onion blight disease caused by Botrytis allii – Mohamed M A Hussein – Egyptian Journal of Biological Pest Control

Ectomycorrhizal fungi may not act as a barrier inhibiting host plant absorption of heavy metals – Yangze Tang – Chemosphere

The impacts of deglaciation and human activity on the taxonomic structure of prokaryotic communities in Antarctic soils on King George Island – E.V. Pershina – Antarctic Science

Fungal, Bacterial, and Archaeal Diversity in Soils Beneath Native and Introduced Plants in Fiji, South Pacific – Gian Maria Niccolò Benucci – Microbial Ecology

Mangrove Sediment Microbiome: Adaptive Microbial Assemblages and Their Routed Biogeochemical Processes in Yunxiao Mangrove National Nature Reserve, China – Xiaolan Lin – Microbial Ecology

Draft Genome Sequence of Burkholderia reimsis BE51, a Plant-Associated Bacterium Isolated from Agricultural Rhizosphere – Qassim Esmaeel – Microbiology Resource Announcements

Rhizosphere microbial response to multiple metal(loid)s in different contaminated arable soils indicates crop-specific metal-microbe interactions – Weimin Sun – Applied and Environmental Microbiology

Draft Genome Sequence of Burkholderia reimsis BE51, a Plant-Associated Bacterium Isolated from Agricultural Rhizosphere – Qassim Esmaeel – Microbiology Resource Announcements

Rhizosphere microbial response to multiple metal(loid)s in different contaminated arable soils indicates crop-specific metal-microbe interactions – Weimin Sun – Applied and Environmental Microbiology

Apple rootstocks of different nitrogen tolerance affect the rhizosphere bacterial community composition – Xiaofen Chai – Journal of Applied Microbiology

Draft Genome Sequence of Pseudomonas sp. Strain MWU13-2860, Isolated from a Wild Cranberry Bog in Truro, Massachusetts – Ghazal Ebadzadsahrai – Microbiology Resource Announcements

Biotechnological potential of plant growth-promoting bacteria from the roots and rhizospheres of endemic plants in ironstone vegetation in southeastern Brazil – Érica Barbosa Felestrino – World Journal of Microbiology and Biotechnology

Effects of consecutive monoculture of sweet potato on soil bacterial community as determined by pyrosequencing – Huan Li – Journal of Basic Microbiology

Air and waterborne microbiome of a pharmaceutical plant provide insights on spatiotemporal variations and community resilience after disturbance – Filippo Pacchioni – BMC Microbiology

Spatial variability of microbial communities in a fractured sedimentary rock matrix impacted by a mixed organics plume – Gláucia da P. Lima – Journal of Contaminant Hydrology

Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions – Xihui Xu – The ISME Journal

Root growth, function and rhizosphere microbiome analyses show local rather than systemic effects in apple plant response to replant disease soil – Maik Lucas – PLOS One

Rhizosphere microbiome structure alters to enable wilt resistance in tomato – Min-Jung Kwak – Nature Biotechnology

Soil microbial community structure in the rhizosphere of Robinia pseudoacacia L. seedlings exposed to elevated air temperature and cadmium-contaminated soils for 4 years – X.Jia – Science of the Total Environment

Water and extremophile microbiome

Desiccation- and Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments – Steffi Genderjahn – Frontiers in Microbiology

Air and waterborne microbiome of a pharmaceutical plant provide insights on spatiotemporal variations and community resilience after disturbance – Filippo Pacchioni – BMC Microbiology

High diversity of thermophilic cyanobacteria in Rupite hot spring identified by microscopy, cultivation, single-cell PCR and amplicon sequencing – Otakar Strunecký – Extremophiles

Structure of Microbial Mats in the Mramornaya Bay (Crimea) Coastal Areas – N. V. Pimenov – Microbiology

Characterization of a novel bacteriophage specific to Exiguobacterium indicum isolated from a plateau eutrophic lake – Shiying Zhang – Journal of Basic Biology

Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles – Sheila Podell – The ISME Journal

The impact of iron nanoparticles on technetium-contaminated groundwater and sediment microbial communities – Laura Newsome – Journal of Hazardous Materials

Microbial diversity and antibiotic resistance in a final effluent-receiving lake – Kinga Bondarczuk – Science of the Total Environment

Reduced chlorine in drinking water distribution systems impacts bacterial biodiversity in biofilms – Claire Bertelli – Frontiers in Microbiology

Microbial Ecology

A Microbial Saga: How to Study an Unexpected Hot Spot of Microbial Biodiversity from Scratch? – Valeria Souza – Cuatro Ciénegas Ecology, Natural History and Microbiology

How Divergent Is the Cuatro Ciénegas Oasis? Genomic Studies of Microbial Populations and Niche Differentiation – Zulema Gomez-Lunar – Cuatro Ciénegas Ecology, Natural History and Microbiology

Trace metals supplementation enhanced microbiota and biohythane production by two-stage thermophilic fermentation – Chonticha Mamimin – International Journal of Hydrogen Energy

Microcosms and Mesocosms: A Way to Test the Resilience of Microbial Communities in Cuatro Ciénegas – Nguyen E. López-Lozano – Cuatro Ciénegas Ecology, Natural History and Microbiology

Resistome

Candida albicans biofilm–induced vesicles confer drug resistance through matrix biogenesis – Robert Zarnowski – PLOS One

Microbes in space

Comparing Spore Resistance of Bacillus Strains Isolated from Hydrothermal Vents and Spacecraft Assembly Facilities to Environmental Stressors and Decontamination Treatments – Vincenzo Zammuto – Mary Ann Liebert Publishers

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Probiotics / prebiotics

Understanding mode of action can drive the translational pipeline towards more reliable health benefits for probiotics – Michiel Kleerebezem – Current Opinion in Biotechnology

Systematic review with meta‐analysis: the efficacy of prebiotics, probiotics, synbiotics and antibiotics in irritable bowel syndrome – Alexander C. Ford – Alimentary Pharmacology and Therapeutics

Phages and viruses

Characterization of dog serum virome from Northeastern Brazil – M.N.Weber – Virology

Hyperdiverse Viral Communities in an Oligotrophic Oasis (Cuatro Ciénegas): Marine Affinities and Microgeographic Differentiation – P. Isa – Cuatro Ciénegas Ecology, Natural History and Microbiology

Bioinformatics

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes – I-Min A Chen – Nucleic Acids Research

Strain-GeMS: Optimized subspecies identification from microbiome data based on accurate variant modeling – Chongyang Tan – Bioinformatics

Strain-GeMS: Optimized subspecies identification from microbiome data based on accurate variant modeling – Chongyang Tan – Bioinformatics

 

 

October 3, 2018

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Enjoy Reading today’s Microbiome Digest blog focusing on the research articles covering the techniques, what and how treatments alter the microbiome, potential of mycobiome to produce fuels and chemicals, pathogenic functions, gut microbiome, animal microbiome, soil microbiome, Maternal Immune Activation(MIA) and its effect and probiotics from vaginal microbiome. 

TECHNIQUES:

Sequential Isolation of DNA, RNA, Protein, and Metabolite Fractions from Murine Organs and Intestinal Contents for Integrated Omics of Host–Microbiota Interactions – Pranjul Shah – Microbial Proteomics

A primer on investigating the role of the microbiome in brain and cognitive development – Caroline Kelsey – Developmental Psychobiology

TREATMENTS:

Roux-Y Gastric Bypass and Sleeve Gastrectomy directly change gut microbiota composition independent of operation type – Fernanda L. Paganelli – bioRxiv

Review – Systematic review on the first line treatment of amphotericin B in critically ill adults with candidemia or invasive candidiasis – Sean Keane – Expert Review of Anti-infective Therapy

Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant – Ying Taur – Gut Microbiota

Review – Reciprocal interactions between resveratrol and gut microbiota deepen our understanding of molecular mechanisms underlying its health benefits – LiangShen – Trends in Food Science & Technology

Synbiotics modulate gut microbiota and reduce enteritis and ventilator-associated pneumonia in patients with sepsis: a randomized controlled trial – Kentaro Shimizu – Critical Care

MICROBIAL ACTIVITY:

Relief from nitrogen starvation entails quick unexpected down-regulation of glycolytic/lipid metabolism genes in enological Saccharomyces cerevisiae– Catherine Tesnière – bioRxiv

ANTIMICROBIAL RESISTANCE:

Widespread Antibiotic, Biocide, and Metal Resistance in Microbial Communities Inhabiting a Municipal Waste Environment and Anthropogenically Impacted River – Aneisha M. Collins – Applied and Environmental Science

SOIL MICROBIOME:

Book Chapter – Paddy Soil Microbial Diversity and Enzymatic Activity in Relation to Pollution – Muhammad Afzaal – Environmental Pollution of Paddy Soils

Effect of Different Soil Phosphate Sources on the Active Bacterial Microbiota Is Greater in the Rhizosphere than in the Endorhiza of Barley (Hordeum vulgare L.) – Massimiliano Cardinale – Microbial Ecology

URINARY MICROBIOME:

Review – The Role of Urinary Microbiota in Lower Urinary Tract Dysfunction: A Systematic Review – TiagoAntunes-Lopes – European Urology Focus

ANIMAL MICROBIOME:

Ecological patterns in the skin microbiota of frogs from tropical Australia – Keith Christian – Ecology and Evolution

Oral Microbiota of the Snake Bothrops lanceolatus in Martinique – Dabor Résière – Int J Environ Res Public Health

MYCOBIOME:

Draft Genome Assemblies of Five Robust Yarrowia lipolytica Strains Exhibiting High Lipid Production, Pentose Sugar Utilization, and Sugar Alcohol Secretion from Undetoxified Lignocellulosic Biomass Hydrolysates – Caleb Walker – Genome Sequences

GENERAL MICROBIOME:

Book Chapter – The Role and Future Possibilities of Next-Generation Sequencing in Studying Microbial Diversity – VijayNema – Microbial Diversity in the Genomic Era

GUT MICROBIOME:

Review – Association of obesity, diabetes and linked complications with gut microbiota – Amina Arif – Pure and Applied Biology

Bifidobacterial Dominance of the Gut in Early Life and Acquisition of Antimicrobial Resistance – Diana H. Taft – Clinical Science and Epidemiology

The Gut Microbiota in the Pathogenesis and Therapeutics of Inflammatory Bowel Disease – Tao Zuo – Frontiers in Microbiology

Influence of maternal factors on the rumen microbiome and subsequent host performance – Hannah C. Cunningham – Translational Animal Science

Colorectal carcinogenesis: an archetype of gut microbiota–host interaction – James L Alexander – Ecancermedicalscience

ANIMAL MODELS MICROBIOME:

Maternal Immune Activation Alters Adult Behavior, Gut Microbiome and Juvenile Brain Oscillations in Ferrets – Yuhui Li – eNeuro

PROBIOTICS:
Bacteriocin production of the probiotic Lactobacillus acidophilus KS400 – C. Gaspar – AMB Express

October 02, 2018

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Today’s digest features a study on altered gut microbial composition in persons with chronic schizophrenia, a review of different approaches for discovering radical-dependent enzymes in the human gut microbiota and Nature podcast with the latest science news. Happy reading/listening!

Gut microbiome

*Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects – Tanya T. Nguyen – Schizophrenia Research

*Review: Discovering radical-dependent enzymes in the human gut microbiota – Benjamin J Levin and Emily P Balskus – Current Opinion in Chemical Biology

Review: Air Pollution, Early Life Microbiome, and Development – Yvonne Vallès and M. Pilar Francino – Current Environmental Health Reports

Review: The implementation of omics technologies in cancer microbiome research – Benjamin H Mullish – Ecancermedicalscience

Skin microbiome

Skin microbiome modulation induced by probiotic solutions – Bernhard Paetzold – bioRxiv

Vaginal microbiome

Review: Alternative and complementary therapies for vulvovaginal candidiasis – Thais Chimati Felix – Folia Microbiologica

Animal microbiome

Review: Fish Gut Microbiome: Current Approaches and Future Perspectives – Chandni Talwar – Indian Journal of Microbiology

Review: The application of omics to rumen microbiota function – Stuart E Denman – Animal

Animal experiments

The circadian clock regulates the diurnal levels of microbial short‐chain fatty acids and their rhythmic effects on colon contractility in mice – Anneleen Segers – Acta Physiologie

Bioinformatics

Dynamic interaction network inference from longitudinal microbiome data – Jose Lugo-Martinez – bioRxiv

Microbes in the news

6 Artificial Sweeteners That Can Hurt Your Microbiome Revealed in New Study – By Emma Betuel – Inverse

Study: Measuring Artificial Sweeteners Toxicity Using a Bioluminescent Bacterial Panel – Dorin Harpaz – Molecules

Podcast

*A wearable biosensor and a metamaterial’s strange behaviour – Benjamin Thompson and Shamini Bundell – Nature Podcast

October 1, 2018

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To kick off October, we have a Microbiome Digest filled with ecological approaches to microbial communities and techniques for analysis. Plus: what the Nobels are doing to encourage diversity, and what ecstasy does to octopuses. Happy reading!

General Microbiome
Neutral and selective dynamics in a synthetic microbial community. – Nate J. Cira – PNAS

Microbiomes as Metacommunities: Understanding Host-Associated Microbes through Metacommunity Ecology. – Elizabeth Theresa Miller – Trends in Ecology and Evolution

Clinician Guide to Microbiome Testing – Christopher Staley – Digestive Diseases and Sciences

Human Urinary Microbiome
NMR-based metabonomic approach reveals changes in the urinary and fecal metabolome caused by resveratrol. – Gabriela Torres Santiago – Journal of Pharmaceutical and Biomedical Analysis

Urinary microbes and postoperative urinary tract infection risk in urogynecologic surgical patients – Krystal J. Thomas-White – International Urogynecology Journal

Human Gut Microbiome
Metagenomic insights into resistant starch degradation by human gut microbiota. – Marius Vital – Applied and Environmental Microbiology

Pathogenic functions of host microbiota. – Silke Rath – Microbiome

Prebiotics and Probiotics in Digestive Health – Eamonn M.M. Quigley – Clinical Gastroenterology and Hepatology

Animal Experiments
Isolation and characterization of the Bacillus cereus BC7 strain, which is capable of zearalenone removal and intestinal flora modulation in mice. – Yue Wang – Toxicon

Sulfated Polysaccharide from Sea Cucumber and its Depolymerized Derivative Prevent Obesity in Association with Modification of Gut Microbiota in High‐Fat Diet‐Fed Mice – Zhenjun Zhu – Molecular Nutrition and Food Research

Animal Microbiome
Cultivable microbiome and its resistance to antimicrobials isolated from Zaprionus indianus – Graziele Aparecida Fernandes da Cruz – Environmental Monitoring and Assessment

Plant, root, and soil microbiome
Impact of weather conditions, leaf age and irrigation water disinfection on the major epiphytic bacterial genera of baby spinach grown in an open field – Pilar Truchado – Food Microbiology

Influence of light on plant – phyllosphere interaction – Sofia D. Carvalho – Frontiers in Plant Science

Techniques
PCR-based quantification of taxa-specific abundances in microbial communities: Quantifying and avoiding common pitfalls. – Fabian Bonk – Journal of Microbiological Methods

Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes. – Johannes Alneberg – Microbiome

Progress of analytical tools and techniques for human gut microbiome research – Eun-Ji Song – Journal of Microbiology

Preprint: Dynamic interaction network inference from longitudinal microbiome data – Jose Lugo-Martinez – bioRxiv

Science, Publishing, and Career
What the Nobels are — and aren’t — doing to encourage diversity – Elizabeth Gibney -Nature

Alyson’s Non-Microbiology Pick
What Ecstasy Does to Octopuses – Ed Yong – The Atlantic

September 28, 2018

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Happy Friday! Today we have a long Digest with several interesting reviews and preprints. Learn about the fallopian tube microbiome, the bacterial communities in Icelandic volcanic deposits, the effect of ammonia on anaerobic digesters, skin defense peptides that modulate a frog’s resistance to a pathogen, and a new tool for constructing pan-genomes from shotgun metagenomic data. Enjoy!

General Microbiome
The mammalian mycobiome: A complex system in a dynamic relationship with the host
– Ghee Chuan Lai – WIREs Systems Biology and Medicine

Niche and fitness differences determine invasion success and impact in laboratory bacterial communities. – Shao-peng Li – ISMEJ

Pregnancy and Early Life
Fallopian tube microbiota: evidence beyond DNA. -Elise S Pelter – Future Microbiology

Human Oral Microbiome
Titanium as a modifier of the peri‐implant microbiome structure – Diane Daubert – Clinical Implant Dentistry and Related Research

Human Gut Microbiome
Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis. – Yan He – Microbiome

Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease – Federica Ungaro – Gut Microbes

Obesity-Linked Gut Microbiome Dysbiosis Associated with Derangements in Gut Permeability and Intestinal Cellular Homeostasis Independent of Diet. – Ravinder Nagpal – Journal of Diabetes Research

Preprint: Social relationships, social isolation, and the human gut microbiota – Kimberly Dill-McFarland – bioRxiv

Review: Gut Microbiota: IgA Protects the Pioneers – Whitman B. Schofield – Current Biology

Review: The Gut Microbiota and Dysbiosis in Autism Spectrum Disorders. – Heather K. Hughes – Current Neurology and Neuroscience Reports

Animal Experiments
Modulation of Pulmonary Microbiota by Antibiotic or Probiotic Aerosol Therapy: A Strategy to Promote Immunosurveillance against Lung Metastases. – Valentino Le Noci – Cell Reports

Nod2 Deficiency in mice is Associated with Microbiota Variation Favouring the Expansion of mucosal CD4+ LAP+ Regulatory Cells – A. Butera – Scientific Reports

Fermented Astragalus in diet altered the composition of fecal microbiota in broiler chickens – Hongxing Qiao – AMB Express

Chronic nonbacterial prostate inflammation in a rat model is associated with changes of gut microbiota that can be modified with a galactoglucomannan‐rich hemicellulose extract in diet – Yvonne Konkol – BJU International

Animal Microbiome
Microbiota and skin defense peptides may facilitate coexistence of two sympatric Andean frog species with a lethal pathogen. – Sandra V. Flechas – ISMEJ

Green forage and fattening duration differentially modulate cecal microbiome of Wanxi white geese. – Xingyong Chen – PLoS One

Plant, root, and soil microbiome
Succession and diversity of microbial communities in landfills with depths and ages and its association with dissolved organic matter and heavy metals. – Si-jia Liu – Science of The Total Environment

Characterization of the bacterial communities on recent Icelandic volcanic deposits of different ages.– Bo Byloos – BMC Microbiology

Linking microbial co-occurrences to soil ecological processes across a woodland-grassland ecotone. – Samiran Banerjee – Ecology and Evolution

Water and Extremophile Microbiome
Independent and interactive effects of reduced seawater pH and oil contamination on subsurface sediment bacterial communities – António Louvado – Environmental Science and Pollution Research

Effects of nutrient enrichment on surface microbial community gene expression in the oligotrophic North Pacific Subtropical Gyre – J. C. Robidart – ISMEJ

Food and Industrial Microbiology
Lacto-fermented sauerkraut improves symptoms in IBS patients independent of product pasteurisation – a pilot study – Elsa Sandberg Nielsen – Food & Function

Relationship between microbial community, operational factors and ammonia inhibition resilience in anaerobic digesters at low and moderate ammonia background concentrations. – Y. Lu – New Biotechnology

Microbial Community Enhances Biodegradation of Bisphenol A Through Selection of Sphingomonadaceae. – Seungdae Oh – Microbial Ecology

Bioinformatics
MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data. – Florian Plaza Oñate – Bioinformatics

Preprint: A unified framework for unconstrained and constrained ordination of microbiome read count data – Stijn Hawinkel – bioRxiv