April 17, 2019

Today’s Digest contains quite a few news articles. Features for today include a review on the importance of proper controls in microbiome studies, a patent for one method of analyzing microbiome dynamics (really?), and the NASA Twins Study, how can one year in space change your gut microbiota and much more? Enjoy reading!

General microbiology

Guideline: Microbiology Investigation Criteria for Reporting Objectively (MICRO): a framework for the reporting and interpretation of clinical microbiology data – Paul Turner & Andrew Fox-Lewis et al. – BMC Medicine

** Patent: Method of analyzing microbiome – E Segal & E Elinav

Combined deterministic and stochastic processes control microbial succession in replicate granular biofilm reactors – R Liébana et al. – Environmental Science & Technology

** Uncorrected proof: Issues and current standards of controls in microbiome research – Bastian V.H. Hornung et al. – FEMS Microbiology Ecology

Pregnancy and early life

Review: Intestinal Microbiota in Early Life and Its Implications on Childhood Health – Lu Zhuang et al. – Genomics, Proteomics & Bioinformatics

Cancer microbiome

PDF: Gastric Microbiota in Helicobacter pylori-Negative and -Positive Gastritis Among High Incidence of Gastric Cancer Area – Boldbaatar Gantuya et al. – Cancers

Human respiratory microbiome

Review: Microbes, metabolites, and the gut–lung axis – Anh Thu Dang & Benjamin J. Marsland – Mucosal Immunology

Microbial contributions to bronchial asthma occurrence in children: A metagenomic study – Man Tian et al. – Journal of Cellular Biochemistry

Human gut microbiome

Review: A Review on Bile Acids: Effects of the Gut Microbiome, Interactions with Dietary Fiber, and Alterations in the Bioaccessibility of Bioactive Compounds – Jashbir Singh et al. – Journal of Agricultural and Food Chemistry

Increased mucosal neutrophil survival is associated with altered microbiota in HIV infection – Tiffany Hensley-McBain et al. – PLoS Pathogens

Review: Thinking bigger: How early life environmental exposures shape the gut microbiome and influence the development of asthma and allergic disease – Hind Sbihi et al. – Allergy

** The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight – Francine E. Garrett-Bakelman et al. – Science


Review: Changes in the Human Metabolome Associated With Alcohol Use: A Review – Taija Voutilainen & Olli Kärkkäinen – Alcohol and Alcoholism

Animal microbiome

Dynamic changes in rumen fermentation and bacterial community following rumen fluid transplantation in a sheep model of rumen acidosis: implications for rumen health in ruminants – Junhua Liu et al. – The FASEB Journal

Rainbow trout (Oncorhynchus mykiss) gut microbiota is modulated by insect meal from Hermetia illucens prepupae in the diet – Genciana Terova et al. – Reviews in Fish Biology and Fisheries

Plant, root and soil microbiome

Effects of mycorrhizae and water conditions on perennial ryegrass growth in rare earth tailings – Qiao Yang et al. – RSC Advance

Niche separation of species of entomopathogenic fungi within the genera Metarhizium and Beauveria in different cropping systems in Mexico – J.A. Cabrera-Mora et al. – Fungal Ecology

Soil abiotic properties and plant functional traits mediate associations between soil microbial and plant communities during a secondary forest succession on the Loess Plateau – Yongfu Chai et al. – Frontiers in Microbiology

Microbial Diversity and Antimicrobial Resistance Profile in Microbiota from Soils of Conventional and Organic Farming Systems – Julija Armalytė et al. – Frontiers in Microbiology

Effects of elevated temperature and elevated CO2 on soil nitrification and ammonia-oxidizing microbial communities in field-grown crop – Linh T.T. Nguyen et al. – Science of The Total Environment

Tropical forest conversion to rubber plantation affects soil micro- & mesofaunal community & diversity – Dharmesh Singh et al. – Scientific Reports

Water and extremophile microbiome

Sulfate reduction by a haloalkaliphilic bench-scale sulfate-reducing bioreactor and its bacterial communities at different depths – Tingzhen Mu et al. – Biochemical Engineering Journal

Extremely acidic environment: Biogeochemical effects on algal biofilms – Ana Teresa Luís et al. – Ecotoxicology and Environmental Safety

Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench – Jiwen Liu & Yanfen Zheng et al. – Microbiome

Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges – Rachel Samson et al. – Science of The Total Environment

Distribution of microbial communities in metal-contaminated nearshore sediment from Eastern Guangdong, China – Mei Zhuang et al. – Environmental Pollution

Phages and viruses

Diversities and potential biogeochemical impacts of mangrove soil viruses – Min Jin et al. – Microbiome


Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis – Dongmei Ai et al. – BMC Genomics

Microbes in the news

Can changing the microbiome reverse lactose intolerance? – PATRICIA L. FOSTER – PhillyVoice

A Look at the Trillions of Microorganisms That Live in and on You – Shayla Love – Vice

Mode of delivery alters infants’ gut microbiota and this may impact respiratory health in first year of life – EurekAlert!

Fecal Transplant Reduces Nearly 50 Percent Of Autism Symptoms In Children – Allan Adamson – Tech Times

Edinburgh Science Festival: from gut bacteria and depression to how rice is risking the planet – Helen McArdle – The Herald

Gut microbiome changes emerge as a potential modulator of age-associated cardiovascular disease risk – Andreu Prados – Gut Microbiota for Health

The Gut Microbiome & Cancer Immunotherapy – Osman, Afaf E. G. & Luke, Jason J. – Oncology Times


March 12, 2019

Today’s Digest casts a wide net with focuses on antibiotic resistance , human gut microbiome and microbiome in extreme environments. Highlights include a review on fungi in the marine environment, a report on gut mucosal virome alterations in ulcerative colitis and finally, sleep well!

General microbiology

Review: Transcription in cyanobacteria: a distinctive machinery and putative mechanisms – Amber Riaz-Bradley – Biochemical Society Transactions

Preprint: How sample heterogeneity can obscure the signal of microbial interactions – David W. Armitage & Stuart E. Jones – bioRxiv

Behavioral heterogeneity in quorum sensing can stabilize social cooperation in microbial populations – Kelei Zhao et al. – BMC Biology

Antibiotic resistance

Antimicrobial photodynamic activity of toluidine blue encapsulated in mesoporous silica nanoparticles against Pseudomonas aeruginosa and Staphylococcus aureus – Paramanantham Parasuraman et al. – Biofouling

Metaphire guillelmi gut as hospitable micro-environment for the potential transmission of antibiotic resistance genes – Huizhen Chao et al. – Science of The Total Environment

Abundance of antibiotic resistance genes and their association with bacterial communities in activated sludge of wastewater treatment plants: Geographical distribution and network analysis – Haihan Zhang et al. – Journal of Environmental Sciences

Cationic Intrinsically Disordered Antimicrobial Peptides (CIDAMPs) Represent a New Paradigm of Innate Defense with a Potential for Novel Anti-Infectives – Ties Latendorf et al. – Scientific Reports

Preprint: Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance in a model gut microbiota – Andres Aranda-Diaz et al. – bioRxiv

Human oral microbiome

** Sleep deprivation and a non–24-h working schedule lead to extensive alterations in physiology and behavior – Huan Ma et al. – FASEB J

Human gut microbiome

Review: Microbe-metabolite-host axis, two-way action in the pathogenesis and treatment of human autoimmunity – Xiang Meng et al. – Autoimmunity Reviews

Pearls: Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract – Matthew H. Foley et al. – PLoS Pathogens

Review: Biomarkers for Immune Therapy in Gastrointestinal Cancers – Benjamin A. Weinberg et al. – Clinical Advances in Hematology & Oncology

Microbiota Diversity in Human Colorectal Cancer Tissues Is Associated with Clinicopathological Features – Yaxin Wu et al. – Nutrition and Cancer

Review: The microbiome, cancer, and cancer therapy – Beth A. Helmink et al. – Nature Medicine

Correlations of the Gastric and Duodenal Microbiota with Histological, Endoscopic, and Symptomatic Gastritis – Hye Seung Han et al. – Journal of Clinical Medicine

Gut-microbe-braint axis

Research Highlight: Depression linked to the microbiome – Hannah Stower – Nature Medicine

Animal experiments

Differential Sensitivity to Plasmodium yoelii Infection in C57BL/6 Mice Impacts Gut-Liver Axis Homeostasis – Joshua E. Denny et al. – Scientific Reports

Metabolic footprint and intestinal microbial changes in response to dietary proteins in a pig model – Alexandra Schutkowski et al. – Journal of Nutritional Biochemistry

Alterations of Bile Acids and Gut Microbiota in Obesity Induced by High Fat Diet in Rat Model – Hong Lin et al. – Journal of Agricultural and Food Chemistry

Effects of lifelong intake of lemon polyphenols on aging and intestinal microbiome in the senescence-accelerated mouse prone 1 (SAMP1) – Chikako Shimizu et al. – Scientific Reports

Effect of green tea and mulberry leaf powders on the gut microbiota of chicken – Yuan Chen et al. – BMC Veterinary Research

Animal microbiome

Fiddler crab bioturbation determines consistent changes in bacterial communities across contrasting environmental conditions – Jenny Marie Booth & Marco Fusi et al. – Scientific Reports

Plant, root and soil microbiome

Hypotheses: Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration – Radhey Shyam Sharma et al. – Ecology and Evolution

Native and Invading Yellow Starthistle (Centaurea solstitialis) Microbiomes Differ in Composition and Diversity of Bacteria – Patricia Lu-Irving et al. – mSphere

Small molecule reaction networks that model the ROS dynamics of the rhizosphere – Olga Taran et al. – Chemical Communications

Soil HONO emissions at high moisture content are driven by microbial nitrate reduction to nitrite: tackling the HONO puzzle – Dianming Wu et al. – The ISME Journal

Evidence of within-species specialization by soil microbes and the implications for plant community diversity – Jenalle L. Eck et al. – PNAS

Effects of four years of elevated ozone on microbial biomass and extracellular enzyme activities in a semi-natural grassland – Jinyang Wang et al. – Science of The Total Environment

Water and extremophile microbiome

Surveying of acid-tolerant thermophilic lignocellulolytic fungi in Vietnam reveals surprisingly high genetic diversity – Vu Nguyen Thanh et al. – Scientific Reports

Radioactive environment adapted bacterial communities constituting the biofilms of hydrothermal spring caves (Budapest, Hungary) – Nóra Tünde Enyedi et al. – Journal of Environmental Radioactivity

COD/sulfate ratio does not affect the methane yield and microbial diversity in anaerobic digesters – Zeynep Cetecioglu et al. – Water Research

** Review: Fungi in the Marine Environment: Open Questions and Unsolved Problems – Anthony Amend et al. – mBio

Holocene paleodepositional changes reflected in the sedimentary microbiome of the Black Sea – Kuldeep D. More et al. – Geobiology

Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents – Lucy C. Stewart et al. – The ISME Journal

Prebiotics, probiotics and synbiotics

Review: Potential prebiotics and their transmission mechanisms: Recent approaches – Ishu Khangwal & Pratyoosh Shukla – Journal of Food and Drug Analysis

A Preventive Prebiotic Supplementation Improves the Sweet Taste Perception in Diet-Induced Obese Mice – Arnaud Bernard et al. – Nutrients

Phages and viruses

Pancreas of coxsackie virus infected dams and their challenged pups: A complex issue – Sona Sarmirova et al. – Virulence

Preprint: Clades of huge phage from across Earth’s ecosystems – Basem Al-Shayeb et al. – bioRxiv

** Gut mucosal virome alterations in ulcerative colitis – Tao Zuo et al. – Gut


MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches – Weizhi Song et al. – Microbiome

Scientific Communication and Education

Preprint: The life of P.I. – Transitions to Independence in Academia – Sophie E Acton et al. – bioRxiv

March 5, 2019

A rich Digest for your Tuesday. Microbiome distinguishes atopic dermatitis from allergy, viruses hitchhike insect sperm for paternal transmission, and researchers test biofilms as water quality biosensor. Enjoy!


2017 NIH-wide workshop report on “The Human Microbiome: Emerging Themes at the Horizon of the 21st Century” – The 2017 NIH-wide microbiome workshop writing team – Microbiome

General microbiology

Adaptive laboratory evolution of a genome-reduced Escherichia coli – Donghui Choe et al. – Nature Communications

Frequency of disturbance alters diversity, function, and underlying assembly mechanisms of complex bacterial communities – Ezequiel Santillan et al. – npj Biofilms and Microbiomes

Interactions in self-assembled microbial communities saturate with diversity – Xiaoqian Yu et al. – The ISME Journal

Redox traits characterize the organization of global microbial communities – Salvador Ramírez-Flandes – PNAS

The genetic basis for adaptation of model-designed syntrophic co-cultures – Colton J. Lloyd et al. – PLoS Computational Biology

Antimicrobial resistance

Antibiotic resistance in urban runoff – Ayad Almakki et al. – Science of The Total Environment

Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters – Pablo Fresia et al. – Microbiome

Pregnancy and early life

Longitudinal Microbiome Composition and Stability Correlate with Increased Weight and Length of Very-Low-Birth-Weight Infants – Alyson L. Yee et al. – mSystems

Human skin microbiome

** The nonlesional skin surface distinguishes atopic dermatitis with food allergy as a unique endotype – Donald Y. M. Leung et al. – Science Translational Medicine

Inverse association between the skin and oral microbiota in atopic dermatitis – Wei Li et al. – Journal of Investigative Dermatology

Dysbiosis of skin microbiota in psoriatic patients: co-occurrence of fungal and bacterial communities – Zuzana Stehlikova et al. – Frontiers in Microbiology

Human oral microbiome

Specific Gut and Salivary Microbiota Patterns Are Linked With Different Cognitive Testing Strategies in Minimal Hepatic Encephalopathy – Jasmohan Baja et al. – The American Journal of Gastroenterology

Human respiratory microbiome

A Haemophilus sp. dominates the microbiota of sputum from UK adults with non-severe community acquired pneumonia and chronic lung disease – Daniel G. Wootton et al. – Scientific Reports

Review: The Challenging Road of Moving from Association to Causation for Microbiome Research in IPF – Leopoldo N. Segal & Philip L Molyneaux – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Molecular characterization of multidrug-resistant Pseudomonas aeruginosa isolates in hospitals in Myanmar – Tatsuya Tada et al. – Antimicrobial Agents and Chemotherapy

The Dimension of Time in Host-Microbiome Interactions – Giulia T. Uhr et al. – mSystems

The influence of probiotic bacteria and human gut microorganisms causing opportunistic infections on Blastocystis ST3 – M. Lepczyńska & E. Dzika – Gut Pathogens

Human gut-microbiome-brain axis

Review: Systematic Review of Gut Microbiota and Major Depression – Stephanie G. Cheung et al. – Frontiers in Psychiatry

Human multi-site microbiome

Influences on allergic mechanisms through gut, lung, and skin microbiome exposures – Andrea M. Kemter & Cathryn R. Nagler – The Journal of Clinical Investigation

Animal experiments

Metabolic and gut microbial characterization of obesity-prone mice under high-fat diet – Yu Gu et al. – Journal of Proteome Research

Mouse: Impact of 5 Fluorouracil Chemotherapy on Gut Inflammation, Functional Parameters, and Gut Microbiota – A.T.Sougiannis et al. – Brain, Behavior, and Immunity

Mouse: Antigen-presenting ILC3 regulate T cell–dependent IgA responses to colonic mucosal bacteria – Felipe Melo-Gonzalez et al. – Journal of Experimental Medicine

Animal microbiome

Host plant and population source drive diversity of microbial gut communities in two polyphagous insects – Asher G. Jones et al. – Scientific Reports

Bacterial Community of the Digestive Tract of the European Medicinal Leech (Hirudo verbana) from the Danube River – Saraswoti Neupane et al. – Microbial Ecology

Gut microbiota of the European Brown Hare (Lepus europaeus) – G. L. Stalder et al. – Scientific Reports

Plant, root and soil microbiome

Soil microbial functions are affected by organic matter removal in temperate deciduous forest – François Maillard et al. – Soil Biology and Biochemistry

Warming counteracts grazing effects on the functional structure of the soil microbial community in a Tibetan grassland – Li Tang et al. – Soil Biology and Biochemistry

Soil Bacterial Communities From the Chilean Andean Highlands: Taxonomic Composition and Culturability – Felipe Maza et al. – Frontiers in Bioengineering and Biotechnology

Foliar Application of Vegetal-Derived Bioactive Compounds Stimulates the Growth of Beneficial Bacteria and Enhances Microbiome Biodiversity in Lettuce – Francesca Luziatelli et al. – Frontiers in Plant Science

Creek to Table: Tracking fecal indicator bacteria, bacterial pathogens, and total bacterial communities from irrigation water to kale and radish crops – Sarah M.Allard et al. – Science of The Total Environment

Water and extremophile microbiome

Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments – Adrien Vigneron et al. – mSystems

Diversity, spatial distribution and activity of fungi in freshwater ecosystems – Cécile Lepère​ et al. – PeerJ

Spatial variability of Antarctic surface snow bacterial communities – Lucie A. Malard et al. – Frontiers in Microbiology

Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network – Keith Bouma-Gregson et al. – The ISME Journal

Vertical stratification of bacteria and archaea in sediments of a small boreal humic lake – Antti J Rissanen et al. – FEMS Microbiology Letters

Airborne Microbial Communities at High-Altitude and Suburban Sites in Toyama, Japan Suggest a New Perspective for Bioprospecting – Daisuke Tanaka et al. – Frontiers in Bioengineering and Biotechnology

Coral microbiome diversity reflects mass coral bleaching susceptibility during the 2016 El Niño heat wave – Stephanie G. Gardner et al. – Ecology and Evolution

Phages and viruses

** Viral pathogens hitchhike with insect sperm for paternal transmission – Qianzhuo Mao et al. – Nature Communications

Early respiratory viral infections in infants with cystic fibrosis – Ashley R. Deschamp et al. – Journal of Cystic Fibrosis


** Oxygen-reducing microbial cathodes monitoring toxic shocks in tap water – Antonin Prévoteau et al. – Biosensors and Bioelectronics

Inhibition of methanogens decreased sulfadiazine removal and increased antibiotic resistance gene development in microbial fuel cells – Shuai Zhang et al. – Bioresource Technology

Effect of the extraction and purification of soil DNA and pooling of PCR amplification products on the description of bacterial and archaeal communities – Johan S. Sáenz et al. – Journal of Applied Microbiology

Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling – Zigui Chen et al. – mSystems

Ultrahigh-Throughput Multiplexing and Sequencing of >500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 Platform – Johanna B. Holm et al. – mSystems

Fungal Cells Recovery From Air Samples: A Tale of Loss And Gain – Hamza Mbareche et al. – Applied and Environmental Microbiology


Genome and pan-genome analysis to classify emerging bacteria – Aurélia Caputo et al. – Biology Direct

16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses – Stephen Woloszynek et al. – PLoS Computational Biology

February 26, 2019

Today’s Digest features a discovery of an intestinal archaea inversely associated with asthma, a tracking of surviving bacteria after FMT using 16s and a report on a bat species as a reservoir for antibiotic resistant determinants. Enjoy reading!

General microbiology

Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family – Ilias Lagkouvardos et al. – Microbiome

Description of Janibacter massiliensis sp. nov., cultured from the vaginal discharge of a patient with bacterial vaginosis – Mossaab Maaloum et al. – Antonie van Leeuwenhoek

Preprint: Emergence of stable coexistence in a complex microbial community through metabolic cooperation and spatio-temporal niche partitioning – Sonja Blasche et al. – bioRxiv

Human oral microbiome

Streptococcus Salivarius: A Potential Salivary Biomarker for Orofacial Granulomatosis and Crohn’s Disease? – Rishi M Goel et al. – Inflammatory Bowel Diseases

Human respiratory microbiome

Changes in microbiome diversity following beta-lactam antibiotic treatment are associated with therapeutic versus subtherapeutic antibiotic exposure in cystic fibrosis – Andrea Hahn et al. – Scientific Reports

Human gut microbiome

** Intestinal archaea inversely associated with childhood asthma – David J.M. Barnett et al. – The Journal of Allergy and Clinical Immunology

Alterations in intestinal microbiota of colorectal cancer patients receiving radical surgery combined with adjuvant CapeOx therapy – Cheng Kong et al. – Science China Life Sciences

Immunity, microbiota and kidney disease – Felix Knauf et al. – Nature Reviews Nephrology

The human gut Firmicute Roseburia intestinalis is a primary degrader of dietary β-mannans – Sabina Leanti La Rosa et al. – Nature Communications

** Bacterial viability in faecal transplants: Which bacteria survive? – Lito E. Papanicolas et al. – EBioMedicine

Increased risk of chronic fatigue syndrome in patients with inflammatory bowel disease: a population-based retrospective cohort study – Shin-Yi Tsai et al. – Journal of Translational Medicine

Preprint: Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria that may stimulate TLR4 receptors – Matthew R Olm et al. – bioRxiv

Human gut-microbiome-brain axis

Review: Microbes and Monoamines: Potential Neuropsychiatric Consequences of Dysbiosis – Stephen D. Skolnick & Nigel H. Greig – Trends in Neurosciences


Targeted metabolomics for the quantitative measurement of 9 gut microbiota–host co-metabolites in rat serum, urine and feces by liquid chromatography–tandem mass spectrometry – Yifeng Zeng et al. – Journal of Chromatography B

Untargeted Metabolomics and Inflammatory Markers Profiling in Children With Crohn’s Disease and Ulcerative Colitis—A Preliminary Study – Urszula Daniluk et al. – Inflammatory Bowel Diseases

Animal experiments

Effects of a Saccharomyces cerevisiae fermentation product on liver abscesses, fecal microbiome, and resistome in feedlot cattle raised without antibiotics – Katherine L. Huebner et al. – Scientific Reports

Mouse: Altered Gut Microbiota Activate and Expand Insulin B15-23-Reactive CD8+ T-Cells – James A. Pearson et al. – Diabetes

Xiaoyaosan improves depressive-like behavior in rats with chronic immobilization stress through modulation of the gut microbiota – Hui-Zheng Zhu et al. – Biomedicine & Pharmacotherapy
Animal microbiome

In-feed resin acids reduce matrix metalloproteinase activity in the ileal mucosa of healthy broilers without inducing major effects on the gut microbiota – Marisol Aguirre et al. – Veterinary Research

** Bats as reservoirs of antibiotic resistance determinants: A survey of class 1 integrons in Grey-headed Flying Foxes (Pteropus poliocephalus) – Fiona McDougall et al. – Infection, Genetics and Evolution

Plant, root and soil microbiome

Structural and functional responses of microbial community with respect to salinity levels in a coastal reclamation land – Kiyoon Kim et al. – Applied Soil Ecology

Biosolids and Tillage Practices Influence Soil Bacterial Communities in Dryland Wheat – Daniel C. Schlatter et al. – Microbial Ecology

Metabolic regulation of the maize rhizobiome by benzoxazinoids – T. E. Anne Cotton et al. – The ISME Journal

Above and belowground community strategies respond to different global change drivers – Karen L. Adair et al. – Scientific Reports

Utilization of actinobacteria to enhance the production and quality of date palm (Phoenix dactylifera L.) fruits in a semi-arid environment – Hamada AbdElgawad et al. – Science of The Total Environment

Protura are unique: first evidence of specialized feeding on ectomycorrhizal fungi in soil invertebrates – Sarah L. Bluhm et al. – BMC Ecology

Rotations with Indian Mustard and Wild Rocket Suppressed Cucumber Fusarium Wilt Disease and Changed Rhizosphere Bacterial Communities – Xue Jin et al. – Microorganisms

Water and extremophile microbiome

Change in the microbial community of saline geothermal fluids amended with a scaling inhibitor: effects of heat extraction and nitrate dosage – Anke Westphal et al. – Extremophiles

Genomic and metatranscriptomic analyses of carbon remineralization in an Antarctic polynya – So-Jeong Kim & Jong-Geol Kim et al. – Microbiome

Preprint: Extreme niche partitioning promotes a remarkably high diversity of soil microbiomes across eastern Antarctica – Eden Zhang et al. – bioRxiv

Phages and viruses

Viral metagenomics revealed novel betatorquevirus species in pediatric inpatients with encephalitis/meningoencephalitis from Ghana – Daniel Eibach et al. – Scientific Reports

February 12, 2019

Today’s Digest features a major effect to tackle the dark matter in the human gut microbiome, comparison of 8 methods to extract DNA from the oral cavity that yielded an unexpected result, and the investigation on whether we can predict sex/age by our gut microbiota. Enjoy!

General microbiology

Perspective: Bridging the Holistic-Reductionist Divide in Microbial Ecology – Robin Tecon et al. – mSystems

Microbioime sister journal: Welcome to Animal Microbiome – Sharon A. Huws

Engineering microbial consortia by division of labor – Garrett W. Roell et al. – Microbial Cell Factories

Preprint: Revisiting the evolution and taxonomy of Clostridia, a phylogenomic update – Pablo Cruz-Morales et al. – bioRxiv

Human skin microbiome

Skin Microbiota in Contact Sports Athletes and Selection of Antiseptics for Professional Hygiene – Dilyara S. Martykanova et al. – BioMed Research International

Human oral microbiome

Qualitative and quantitative differences in the subgingival microbiome of the restored and unrestored teeth – Steven W. H. Rademacher et al. – Journal of Periodontal Research

Human respiratory microbiome

Comparison of Subtyping Approaches and the Underlying Drivers of Microbial Signatures for Chronic Rhinosinusitis – Kristi Biswas et al. – mSphere

Human gut microbiome

** 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses – Yuanqiang Zou et al. – Nature Biotechnology

Genomic insights from Monoglobus pectinilyticus: a pectin-degrading specialist bacterium in the human colon – Caroline C. Kim et al. – The ISME Journal

Pinning down the role of common luminal intestinal parasitic protists in human health and disease – status and challenges – Christen Rune Stensvold – Parasitology

Dynamics of the Gut Microbiota in Children Receiving Selective or Total Gut Decontamination Treatment During Hematopoietic Stem Cell Transplantation – Vincent Bekker & Romy D. Zwittink et al. – Biology of Blood and Marrow Transplantation

Fecal Microbiota Transplantation in Patients With Primary Sclerosing Cholangitis: A Pilot Clinical Trial – Jessica Allegretti et al. – The American Journal of Gastroenterology

** Preprint: Age and sex-dependent patterns of gut microbial diversity in human adults – Jacobo de la Cuesta-Zuluaga et al. – bioRxiv

Human reproductive tract microbiome

Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study – Johanna Wiik – BMC Women’s Health

Built environment microbiome

Spatial and seasonal variation of the airborne microbiome in a rapidly developing city of China – Hu Li et al. – Science of the Total Environment

Animal experiments

Synbiotic-driven improvement of metabolic disturbances is associated with changes in the gut microbiome in diet-induced obese mice – Xinxin Ke et al. – Molecular Metabolism

The gut microbiota is largely independent of host genetics in regulating fat deposition in chickens – Chaoliang Wen et al. – The ISME Journal

The Glucoamylase Inhibitor Acarbose Has a Diet-Dependent and Reversible Effect on the Murine Gut Microbiome – Nielsen T. Baxter et al. – mSphere

Animal microbiome

Effects of polyethylene microplastics on the gut microbial community, reproduction and avoidance behaviors of the soil springtail, Folsomia candida – Hui Ju et al. – Environmental Pollution

Effects of host blood meal source on reproductive output, nutrient reserves and gut microbiome of West Nile virus vector Culex quinquefasciatus – Aparna Telang & Jessica Skinner – Journal of Insect Physiology

Plant, root and soil microbiome

Soil microbes alter plant fitness under competition and drought – Connor R. Fitzpatrick et al. – Journal of Evolutionary Biology

Multi-resistant plant growth-promoting actinobacteria and plant root exudates influence Cr(VI) and lindane dissipation – María ZoleicaSimón Solá et al. – Chemosphere

Interactions between Pseudomonas spp. and their role in improving the red pepper plant growth under salinity stress – Sandipan Samaddar et al. – Microbiological Research

Plant Defense by VOC-Induced Microbial Priming – Hongwei Liu & Laura E. Brettell – Trends in Plant Science

Water and extremophile microbiome

Microbial ecology of the cryosphere (glacial and permafrost habitats): current knowledge – Rosa Margesin & Tony Collins – Applied Microbiology and Biotechnology

Unique Patterns and Biogeochemical Relevance of Two-Component Sensing in Marine Bacteria – Noelle A. Held et al. – mSystems

Oil-Spill Triggered Shift in Indigenous Microbial Structure and Functional Dynamics in Different Marine Environmental Matrices – C. S. Neethu et al. – Scientific Reports

An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community – Ke Yu et al. – Microbiome

Effects of biomass pyrolysis derived wood vinegar on microbial activity and communities of activated sludge – Fang Zhang et al. – Bioresource Technology

Anti-seasonal submergence dominates the structure and composition of prokaryotic communities in the riparian zone of the Three Gorges Reservoir, China – Yan Fang et al. – Science of The Total Environment

Phages and viruses

Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems – Vera Bischoff et al. – The ISME Journal

In plaque-mass spectrometry imaging of a bloom-forming alga during viral infection reveals a metabolic shift towards odd-chain fatty acid lipids – Guy Schleyer et al. – Nature Microbiology


The mucosal–luminal interface: an ideal sample to study the mucosa-associated microbiota and the intestinal microbial biogeography – Walid Mottawea et al. – Pediatric Research

Development and application of a HILIC UHPLC-MS method for polar fecal metabolome profiling – Nina Sillner et al. – Journal of Chromatography B

** Evaluation of Oral Cavity DNA Extraction Methods on Bacterial and Fungal Microbiota – Jennifer Rosenbaum et al. – Scientific Reports

Xin’s Non-microbiology pick

Preprint: Where do our graduates go? A toolkit for retrospective and ongoing career outcomes data collection for biomedical PhD students and postdoctoral scholars – Elizabeth A. Silva et al. – bioRxiv

January 29, 2019

Today’s Digest features a defined gut consortium providing protection against pathogen and cancer, a primer on parasitic modulation of host behavior, and an international collaboration all about crAssphage. Enjoy reading and stay warm!

General microbiology

Low molecular weight organic acids enhance the high molecular weight polycyclic aromatic hydrocarbons degradation by bacteria – Anithadevi Kenday Sivaram et al. – Chemosphere

Review: Function of Biohydrogen Metabolism and Related Microbial Communities in Environmental Bioremediation – Ying Teng et al. – Frontiers in Microbiology

Rare Taxa Exhibit Disproportionate Cell-Level Metabolic Activity in Enriched Anaerobic Digestion Microbial Communities – Yangyang Jia et al. – mSystems

Antimicrobial resistance

Rationally designing antisense therapy to keep up with evolving bacterial resistance – Seyfullah Kotil & Eric Jakobsson – PLoS One

Preprint: Bacteriophage resistance alters antibiotic mediated intestinal expansion of enterococci – Anushila Chatterjee et al. – bioRxiv

Preprint: Selection for antibiotic resistance is reduced when embedded in a natural microbial community – Uli Klümper et al. – bioRxiv

Higher Temperatures Do Not Always Achieve Better Antibiotic Resistance Genes Removal in Anaerobic Digestion of Swine Manure – Xu Huang et al. – Applied and Environmental Microbiology

Human respiratory microbiome

Metagenome – Inferred bacterial replication rates in cystic fibrosis airways – Katarzyna Pienkowska et al. – Journal of Cystic Fibrosis

Review: The respiratory microbiota: new insights into pulmonary tuberculosis – Setegn Eshetie & Dick van Soolingen – BMC Infectious Diseases

Human gut microbiome

Taxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome – Ziwei Song et al. – Microbiome

** A defined commensal consortium elicits CD8 T cells and anti-cancer immunity – Takeshi Tanoue et al. – Nature

Press: A gut punch fights cancer and infection – Nathan E. Reticker-Flynn & Edgar G. Engleman – Nature

Faecal microbiota transplant for eradication of multidrug-resistant Enterobacteriaceae: a lesson in applying best practice? – Benjamin H. Mullish et al. – Clinical Microbiology and Infection

Screening-level microbial risk assessment of acute gastrointestinal illness attributable to wastewater treatment systems in Nunavut, Canada – Kiley Daley et al. – Science of The Total Environment

Review: Probiotics: How Effective Are They in the Fight against Obesity? – Kiran Mazloom et al. – Nutrients

The gut microbiota heterogeneity and assembly changes associated with the IBD – Yang Sun et al. – Scientific Reports

Human gut-microbiome-brain axis

Exploration of microbiota targets for major depressive disorder and mood related traits – Yu-Chu Ella Chung et al. – Journal of Psychiatric Research

Food microbiology

Role of Intestinal Microbiota in the Bioavailability and Physiological Functions of Dietary Polyphenols – K Kawabata et al. – Molecules

Review: Dietary Advanced Glycation End Products: Digestion, Metabolism and Modulation of Gut Microbial Ecology – Matthew Snelson & Melinda T. Coughlan

Animal experiments

Intestinal bacteria modulate the foraging behavior of the oriental fruit fly Bactrocera dorsalis (Diptera: Tephritidae) – Mazarin Akami et al. – PLoS One

Effect of ZFN-edited myostatin loss-of-function mutation on gut microbiota in Meishan pigs – Wen-Tao Cui et al. – PLoS One

Oral Candida administration in a Clostridium difficile mouse model worsens disease severity but is attenuated by Bifidobacterium – Wimonrat Panpetch et al. – PLoS One

Gut microbiota affects development and olfactory behavior in Drosophila melanogaster – Huili Qiao et al. – Journal Experimental Biology

Animal microbiome

** Primer: Parasite manipulation of host behavior -David P. Hughes & Frederic Libersat – Current Biology

Effects of the captive and wild environment on diversity of the gut microbiome of deer mice (Peromyscus maniculatus) – Elliott Schmidt et al. – The ISME Journal

A longitudinal assessment of host-microbe-parasite interactions resolves the zebrafish gut microbiome’s link to Pseudocapillaria tomentosa infection and pathology – Christopher A. Gaulke et al. – Microbiome

Microbiota comparison of Pacific white shrimp intestine and sediment at freshwater and marine cultured environment – Lanfen Fan et al. – Science of The Total Environment

T6SS contributes to gut microbiome invasion and killing of an herbivorous pest insect by plant-beneficial Pseudomonas protegens – Jordan Vacheron et al. – The ISME Journal

Genomic diversity landscape of the honey bee gut microbiota – Kirsten M. Ellegaard & Philipp Engel

Dynamics of the gut microbiota in developmental stages of Litopenaeus vannamei reveal its association with body weight – Jiqiang Fan et al. – Scientific Reports

Plant, root and soil microbiome

Forum: Microbiome Applications from Lab to Field: Facing Complexity – Angela Sessitsch, Nikolaus Pfaffenbichler & Birgit Mitter – Trends in Plant Science

Review: Plant growth promoting rhizobacteria in sustainable agriculture: from theoretical to pragmatic approach – Samar Mustafa et al. – Symbiosis

Plant evenness modulates the effect of plant richness on soil bacterial diversity – Yao-Qin Sun et al. – Science of The Total Environment

Water and extremophile microbiome

Taurine Is a Major Carbon and Energy Source for Marine Prokaryotes in the North Atlantic Ocean off the Iberian Peninsula – Elisabeth L. Clifford et al. – Microbial Ecology

Organic matter from Arctic sea-ice loss alters bacterial community structure and function – Graham J. C. Underwood et al. – Nature Climate Change

Review: The unexpected habitat in sewer pipes for the propagation of microbial communities and their imprint on urban waters – Sandra L McLellan & Adélaïde Roguet – Current Opinion in Biotechnology

In situ enrichment of microbial communities on polarized electrodes deployed in alkaline hot springs – Abdelrhman Mohamed et al. – Journal of Power Sources

Genomic and metagenomic insights into the microbial community of a thermal spring – Renato Pedron et al. – Microbiome

Changes in the Active, Dead, and Dormant Microbial Community Structure Across a Pleistocene Permafrost Chronosequence – Alexander Burkert et al. – Applied and Environmental Microbiology

Phages and viruses

Adjunct phage treatment enhances the effectiveness of low antibiotic concentration against Staphylococcus aureus biofilms in vitro – James Dickey & Véronique Perrot – PLoS One

** Preprint: Global phylogeography and ancient evolution of the widespread human gut virus crAssphage – Robert Edwards et al. – bioRxiv


Metabolomics and Microbiomes as Potential Tools to Evaluate the Effects of the Mediterranean Diet – Qi Jin et al. – Nutrients

Effects of sample preservation on marine microbial diversity analysis – Athenia L.Oldham et al. – Journal of Microbiological Methods

January 1, 2019

Happy New Year! 2019 comes with a short Digest featuring a review on metabolic regulation by gut microbiota and a high throughput yeast two-hybrid screening method. May 2019 bring much success and happiness.

General microbiology

Probabilistic modeling of microbial networks for integrating partial quantitative knowledge within the nitrogen cycle – Damien Eveillard et al. – Frontiers in Microbiology

Methods to Watch: Microbial interactions – Lei Tang – Nature Methods

Human gut microbiome

Dietary quality of predominantly traditional diets is associated with blood glucose profiles, but not with total fecal Bifidobacterium in Indonesian women – Shiela Stefani et al. – PLoS One

** Review: Gut microbiota as important modulator of metabolism in health and disease – Xiang-qian Wang et al. – Royal Society of Chemistry Advances

Review: Colonization and probiotic function of Bifidobacterium longum – Chengcheng Zhang et al. – Journal of Functional Foods

Food microbiome

Microbial communities and volatile metabolites in different traditional fermentation starters used for Hong Qu glutinous rice wine – Zi-Rui Huang et al. – Food Research International

Plant, root and soil microbiome

Soil parameters drive the diversity of Citrus sinensis rhizosphere microbiota which exhibits a potential in plant drought stress alleviation – Marwa Cherni et al. – Applied Soil Ecology

Revealing microbial processes and nutrient limitation in soil through ecoenzymatic stoichiometry and glomalin-related soil proteins in a retreating glacier forefield – Yonglei Jiang et al. – Geoderma

Water and extremophile microbiome

Co-occurrence patterns of the microbial community in polycyclic aromatic hydrocarbon-contaminated riverine sediments – Zaisheng Yan et al. – Journal of Hazardous Materials

Addition of algicidal bacterium CZBC1 and molasses to inhibit cyanobacteria and improve microbial communities, water quality and shrimp performance in culture systems – Wujie Xu et al. – Aquaculture

Sludge anaerobic digestion with high concentrations of tetracyclines and sulfonamides: dynamics of microbial communities and change of antibiotic resistance genes – Yang Bai et al. – Bioresource Technology

Temperature dependence of denitrification microbial communities and functional genes in an expanded granular sludge bed reactor treating nitrate-rich wastewater – Runhua Liao et al. – Royal Society of Chemistry Advances

Built environment microbiome

Bacillus species at the Canberra Airport: A comparison of real-time polymerase chain reaction and massively parallel sequencing for identification – M.E. Gahan et al. – Forensic Science International


** A user-friendly platform for yeast two-hybrid library screening using next generation sequencing – Marie-Laure Erffelinck & Bianca Ribeiro et al. – PLoS One