August 24, 2019

This weekend, read about the microbial index of skin health for children with eczema, gut microbiome of koalas, and interactions between the gut bacterial microbiome and virome of rhesus monkey. Happy reading!

General microbiome

Why we need a small data paradigm – Eric B. Hekler – BMC Medicine

Correspondence: The importance of genome sequence quality to microbial comparative genomics – Theo H. M. Smits – BMC Genomics

The applications of Big Data in molecular diagnostics – Yin Kwan Evelyn Wong – Expert Review of Molecular Diagnostics

Tiny Hidden Genes within Our Microbiome – Karin Mittelman & David Burstein – Cell

Skin microbiome

*A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children – Zheng Sun – mSystems

Gut microbiome

Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight – Peng Jiang – Microbiome

Review: Gut Microbiota, Dietary Phytochemicals, and Benefits to Human Health – Ran Yin – Current Pharmacology Reports

Mild cognitive impairment has similar alterations as Alzheimer’s disease in gut microbiota – Binyin Li – Alzheimer’s & Dementia

Design of synthetic microbial consortia for gut microbiota modulation – Jorge F. Vázquez-Castellanos – Current Opinion in Pharmacology

Intestinal microbiota and colorectal cancer: changes in the intestinal microenvironment and their relation to the disease – Sandra Aparecida dos Reis – Journal of Medical Microbiology

Review: Celiac disease: a comprehensive current review – Giacomo Caio – BMC Medicine

Pregnancy and early life

Maternal IgA protects against the development of necrotizing enterocolitis in preterm infants – Kathyayini P. Gopalakrishna – Nature Medicine

Oral microbiome

Oral Microbiome and Cancer Therapy-Induced Oral Mucositis – Jean-Luc C Mougeot – JNCI Monographs

Respiratory microbiome

Deciphering the Ecology of Cystic Fibrosis Bacterial Communities: Towards Systems-Level Integration – Annamaria Bevivino – Trends in Molecular Medicine

Water and extremophile microbiome

Effects of water recirculation rate on the microbial community and water quality in relation to the growth and survival of white shrimp (Litopenaeus vannamei) – Zhao Chen – BMC Microbiology

Pseudomethylobacillus aquaticus gen. nov., sp. nov., a new member of the family Methylophilaceae isolated from an artificial reservoir – Ceshing Sheu – International Journal of Systematic and Evolutionary Microbiology

Bacterial Communities from Extreme Environments: Vulcano Island – Camilla Fagorzi – Diversity

Diversity and biogeography of SAR11 bacteria from the Arctic Ocean – Susanne Kraemer – bioRxiv

Review: Metal and organic pollutants bioremediation by extremophile microorganisms – Patricia Giovanella – Journal of Hazardous Material

Animal microbiome

*Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala – Michaela D. J. Blyton – Animal microbiome

Impact of pine leaf biochar amendment on bacterial dynamics and correlation of environmental factors during pig manure composting – Jiao Li – Bioresource Technology

Animal experiment

Potential roles of gut microbiome and metabolites in modulating ALS in mice – Eran Blacher – Nature

Plant microbiome

Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples – Tonia DeBellis – PeerJ

Non-target Effects of Trichoderma on Plants and Soil Microbial Communities – Monika Jangi – Plant Microbe Interface

Inhibitory and nutrient use phenotypes among co‐existing Fusarium and Streptomyces populations suggest local coevolutionary interactions in soil – Adil Essarioui – Environmental Microbiology

Phages and viruses

*The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites – Heng Li – Virology Journal

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August 20, 2019

Today’s digest includes the gut microbiome of sea turtles, microbes on a guyot in the Pacific Ocean, and a review of microbiome animal models. Enjoy!

General microbiome

Review: Simple animal models for microbiome research – Douglas – Nature Reviews Microbiology

Review: An Ecological Loop: Host Microbiomes across Multitrophic Interactions – Liu – Trends in Ecology & Evolution

Review: The antibody/microbiota interface in health and disease – Sterlin – Mucosal Immunology

Pregnancy and early life

Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria – Casaburi – Antimicrobial Resistance & Infection Control

Human skin microbiome

The prevalence of the culturable human skin aerobic bacteria in Riyadh, Saudi Arabia – Shami – BMC Microbiology

Animal experiments

Oral Administration of Clinically Relevant Antimalarial Drugs Does Not Modify the Murine Gut Microbiota – Denny & Schmidt – Scientific Reports

Animal microbiome

New insights into the gut microbiome in loggerhead sea turtles Caretta caretta stranded on the Mediterranean coast – Arizza – PLoS One

Outcomes of a low birth weight phenotype on piglet gut microbial composition and intestinal transcriptomic profile – Fouhse – Canadian Journal of Animal Science

Plant, root, and soil microbiome

Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia – Pérez-Jaramillo – Microbiome

Preprint: Exploring the microbial diversity in oil-contaminated mangrove sediments using 16S rRNA metagenomics – Ghanbari – BioRxiv

Plant-microorganisms interaction promotes removal of air pollutants in Milan (Italy) urban area – Franzetti – Journal of Hazardous Materials

Effects of natural vegetative restoration on soil fungal and bacterial communities in bare patches of the southern Taihang Mountains – Zhao – Ecology and Evolution

Water and extremophile microbiome

The differentiation of iron-reducing bacterial community and iron-reduction activity between riverine and marine sediments in the Yellow River estuary – Zhang – Marine Life Science & Technology

Bacterial Community on a Guyot in the Northwest Pacific Ocean Influenced by Physical Dynamics and Environmental Variables – Liu – JGR: Biogeosciences

Microdiversity ensures the maintenance of functional microbial communities under changing environmental conditions – García-García – ISME

Built environment

Seasonal diversity of the bacterial communities associated with petroglyphs sites from the Negev Desert, Israel – Nir – Annals of Microbiology

Antibiotic fermentation residue for biohydrogen production using different pretreated cultures: Performance evaluation and microbial community analysis – Yang – Bioresource Technology

Bioinformatics

Metagenomic approaches: effective tools for monitoring the structure and functionality of microbiomes in anaerobic digestion systems – Carabeo-Pérez – Applied Microbiology and Biotechnology

August 19, 2019

Monday’s digest is about microbiota as biomarker in diverse human diseases such as alopecia areata and bladder cancer, how arabinoxylan and grape pomace affects microbiota in rodents and microbial characterization of multi-strain probiotic VSL3 .

General microbiome

What Pediatricians Should Know Before Studying Gut Microbiota – Lorenzo Drago – Journal of Clinical Medicine

The role of gut microbiota for the activity of medicinal plants traditionally used in the European Union for gastrointestinal disorders – Timo A. Thumann – Journal of Ethnopharmacology

Human microbiome

The sex-specific interaction of the microbiome in neurodegenerative diseases – Laura M. Cox – Brain Research

Analysis of the gut microbiota in alopecia areata: identification of bacterial biomarkers – Oscar M. Moreno-Arrenos – Journal of the European Academy of Dermatology and Venereology

The dynamics of the oral microbiome and oral health among patients receiving clear aligner orthodontic treatment – Rui Zhao – Oral Diseases

Urinary microbiota – a potential biomarker and therapeutic target for bladder cancer – Hai Bi – Journal of Medical Microbiology

Animal experiments

Effect of arabinoxylan on colonic bacterial metabolites and mucosal barrier in high‐fat diet‐induced rats – Shanshan Li – Food Science and Nutrition

The Signature Microbiota Driving Rumen Function Shifts in Goat Kids Introduced Solid Diet Regimes – Xiaokang Lv – BioRxiv

Effects of grape pomace and seed polyphenol extracts on the recovery of gut microbiota after antibiotic treatment in high‐fat diet‐fed mice – Feng Lu – Food Science and Nutrition

Microbiota-driven gut vascular barrier disruption is a prerequisite for non-alcoholic steatohepatitis development – Juliette Mouries – Journal of Hepatology

Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows – Yuliaxis Ramayo‐Caldas – Journal of Animal Breeding and Genetics

The gastrointestinal fate of limonin and its effect on gut microbiota in mice – Min Gu – Food and Function

Plant, root, soil microbiome

Environmental pollution effects on plant microbiota: the case study of poplar bacterial-fungal response to silver nanoparticles – Francesco Vitali – Applied Microbiology and Biotechnology

Salinity-induced changes in the rhizosphere microbiome improve salt tolerance of Hibiscus hamabo – Yongge Yuan – Plant and Soil

Water and extremophile microbiome

Metagenomic characterization of creek sediment microbial communities from a major agricultural region in Salinas, California – Brittany J. Suttner – BioRxiv

Probiotics

Development of omics-based protocols for the microbiological characterization of multi-strain formulations marketed as probiotics: the case of VSL#3 – Diego Mora – Microbial Biotechnology

Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial – Xuan He – Scientific Reports

Probiotic L. gasseri strain (LG21) for the upper gastrointestinal tract acting through improvement of indigenous microbiota – Yasuhiro Koga – BMJ Open Gastroenterology

Non Microbiology Picks

First cells may have emerged because building blocks of proteins stabilized membranes – Science Daily

August 10, 2019

This weekend, read about the role that gut microbes play in inflammation, microbes in the placenta-maternal interface, BactMAP R package, and more. Happy reading!

General microbiome

High proportions of bacteria and archaea across most biomes remain uncultured – Andrew D. Steen – The ISME Journal

Isolation of an archaeon at the prokaryote-eukaryote interface – Hiroyuki Imachi – bioRxiv

Urinary microbiome

A Prospective Study of the Urinary and Gastrointestinal Microbiome in Prepubertal Males – Borna Kassir – Urology

Gut microbiome

*Review: The intestinal microbiota fuelling metabolic inflammation – Herbert Tilg – Nature Reviews Immunology

Long-term dietary intervention reveals resilience of the gut microbiota despite changes in diet and weight – Gabriela K Fragiadakis – bioRxiv

Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs – Katharine M. Ng – bioRxiv

Differential detection of Entamoeba species in stool samples collected from children in District Swat, Khyber Pakhtunkhwa Pakistan – Muhammad Iftikhar Khan – bioRxiv

Association network analysis identifies enzymatic components of gut microbiota that significantly differ between colorectal cancer patients and healthy controls – Dongmei Ai – PeerJ

Specific changes in faecal microbiota are associated with familial Mediterranean fever – Samuel Deshayes – Annals of the Rheumatic Diseases

Pregnancy and early life

*Functional characterization of Ralstonia insidiosa, a bona fide resident at the maternal-fetal interface – Lindsay A. Parnell – bioRxiv

The association between caesarean section delivery and later life obesity in 21-24 year olds in an Urban South African birth cohort – Eniola Sogunle – bioRxiv

Water and extremophile microbiome

Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments – Satoshi Hiraoka – bioRxiv

Metabolically-active obligate aerobes in anoxic (sulfidic) marine sediments – Sabyasachi Bhattacharya – bioRxiv

Plant microbiome

Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples – Tonia DeBellis – PeerJ

Non-target Effects of Trichoderma on Plants and Soil Microbial Communities – Monika Jangi – Plant Microbe Interface

Bioinformatics

*BactMAP: an R package for integrating, analyzing and visualizing bacterial microscopy data – Renske van Raaphorst – bioRxiv

Podcast

The placental microbiome, and advances in artificial intelligence – Nick Howe and Noah Baker – Nature Podcast

August 1, 2019

Happy Thursday! Today’s digest includes fungi abundance in paddy fields, the microbial quality of treated wastewater, and the oral microbiome of cats. Enjoy!

Animal microbiome

The feline cutaneous and oral microbiota are influenced by breed and environment – Older – PLoS One

Microbial community modulates growth of symbiotic fungus required for stingless bee metamorphosis – Paludo – PLoS One

Preprint: Effects of the copper IUD on composition of the vaginal microbiota in the olive baboon – Eastman – bioRxiv

Plant, root, and soil microbiome

Nitrogen fertilization altered arbuscular mycorrhizal fungi abundance and soil erosion of paddy fields in the Taihu Lake region of China – Zhang – Environmental Science and Pollution Research

Reconciling disparate responses to grazing in the arbuscular mycorrhizal symbiosis – van Der Heyde – Rhizosphere

Redox-driven shifts in soil microbial community structure in the drawdown zone after construction of the Three Gorges Dam – Wang – Soil Ecology Letters

Water and extremophile microbiome

Biomarker Profiling of Microbial Mats in the Geothermal Band of Cerro Caliente, Deception Island (Antarctica): Life at the Edge of Heat and cold – Lezcano – Astrobiology

Microbial diversity analysis and screening for novel xylanase enzymes from the sediment of the Lobios Hot Spring in Spain – Knapik – Scientific Reports

Built environment

How does urban wastewater treatment affect the microbial quality of treated wastewater? – Lopez – Process Safety and Environmental Protection

Identifying microbial community evolution in membrane bioreactors coupled with anaerobic side-stream reactor, packing carriers and ultrasonication for sludge reduction by linear discriminant analysis – Zheng – Bioresource Technology

Food microbiology

Preprint: Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico – Rocha-Arriaga – bioRxiv

Bioinformatics

Preprint: µbialSim: constraint-based dynamic simulation of complex microbiomes – Popp and Centler – bioRxiv

July 27, 2019

Have a nice weekend! Today, in this Digest, it is worth to remark a study in mice showing the impact of microbiome composition on muscle loss, in addition to a paper presenting the new version of QIIME, one of the most utilized microbiome analysis software available. 

 

Human and General Microbiome

Pearls: Microbiome evolution during host aging – Francisco Daniel Davila Aleman – PLOS Pathogens

Review: The structure and function of the human small intestinal microbiota: Current understanding and future directions – Arthur J. Kastl, Jr – Cellular and Molecular Gastroenterology and Hepatology

Review: The impact of tumor and gut microbiotas on cancer therapy; Beneficial or detrimental? – Yalda Hekmatshoar – Life Sciences 

Review: Gut Microbiota in Phytopharmacology: A Comprehensive Overview Of Concepts, Reciprocal Interactions, Biotransformations And Mode Of Actions – Priyankar Dey – Pharmacological Research

Review: The role of the skin microbiota in acne pathophysiology – S. Ramasamy – British Journal of Dermatology

Review: Study Insights into Gastrointestinal Cancer through the Gut Microbiota – Fanli Kong – BioMed Research International

Review: Contribution of Aging, Obesity, and Microbiota on Tumor Immunotherapy Efficacy and Toxicity – Regina E. M. Baiden-Amissah – International Journal in Molecular Sciences

TARgeting the cutaneous microbiota in atopic dermatitis by coal tar via AHR-dependent induction of antimicrobial peptides – Jos P.H. Smits – Journal of Investigative Dermatology

The Gut Microbiota in Collagenous Colitis Shares Characteristics With Inflammatory Bowel Disease-Associated Dysbiosis – Adam Carstens – Clinical and Translational Gastroenterology

Changes in oral microbial profiles associated with oral squamous cell carcinoma vs leukoplakia – Kengo Hashimoto – Journal of Investigative and Clinical Dentistry

Probiotics modulate the gut microbiota composition and immune responses in patients with atopic dermatitis: a pilot study – Zhifeng Fang – European Journal of Nutrition

Role of Bile Acids in Dysbiosis and Treatment of Nonalcoholic Fatty Liver Disease –  – Caihua Wang – Mediators of Inflammation

Rectal Swabs from Critically Ill Patients Provide Discordant Representations of the Gut  Microbiome Compared to Stool Samples – Katherine Fair – mSphere 

Measurement of gut microbial metabolites in cardiometabolic health and translational research – Wei‐Kai Wu – Rapid Communications in Mass Spectrometry

 

Animal Microbiome and Animal Experiments

The gut microbiota influences skeletal muscle mass and function in mice – Shawon Lahiri – Science Translational Science

Intestinal Clostridium species lower host susceptibility to enterohemorrhagic Escherichia coli O157:H7 infection – Yukako Koyanagi – Pathogens and Disease

Preparation and characterization of selenium enriched-Bifidobacterium longum DD98, and its repairing effects on antibiotic-induced intestinal dysbacteriosis in mice – Hui Zhu – Food and Function 

The Ruminal Microbiome and Metabolome Alterations Associated with Diet-Induced Milk Fat Depression in Dairy Cows – Hongbo Zeng – Metabolites

 

Water Microbiome

Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome:  bacteria, viruses and vesicles matter – Lucia Maestre‐Carballa – Environmental Microbiology

 

Built Environment Microbiome

Identification of city specific important bacterial signature for the MetaSUB CAMDA challenge microbiome data – Alejandro R. Walker – Biology Direct 

 

Plant Microbiome

Genome Evolution and Host Microbiome Shifts Correspond with Intraspecific Niche Divergence within Harmful Algal Bloom-Forming Microcystis aeruginosa – Sara L. Jackrel – Molecular Ecology

Novel insights into plant-associated archaea and their functioning in arugula (Eruca sativa Mill.) – Julian Taffner – Journal of Advanced Research

Seeds of native alpine plants host unique microbial communities embedded in cross-kingdom networks – Birgit Wassermann – Microbiome

 

Bioinformatics

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 – Evan Bolyen – Nature Biotechnology

Friday, July 19th

Happy Friday! Today’s digest includes the microbiome of plankton, viral diversity of ticks, and a review of microbiome engineering. Enjoy!

General microbiome

Homeorhesis and ecological succession quantified in synthetic microbial ecosystems – Chuang – PNAS

Human nearly-sterile sites

Insights into the Microbiome of Breast Implants and Periprosthetic Tissue in Breast Implant-Associated Anaplastic Large Cell Lymphoma – Walker – Scientific Reports

Human gut microbiome

Review: Precision Medicine Goes Microscopic: Engineering the Microbiome to Improve Drug Outcomes – Lam – Cell Host & Microbe

A structured weight loss program increases gut microbiota phylogenetic diversity and reduces levels of Collinsella in obese type 2 diabetics: A pilot study – Frost – PLoS One

Animal experiments

Changes in cecal microbiota community of suckling piglets infected with porcine epidemic diarrhea virus – Tan – PLoS One

Animal microbiome

Cicadae pupa promotes metabolites synthesis of Isaria cicadae, a dominant species in cicada flowers microbiota – Chunyu – Journal of Agricultural and Food Chemistry

Experimental Evidence for Adaptation to Species-Specific Gut Microbiota in House Mice – Moeller – mSphere

Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae – Gaona – PLoS One

Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection – Kolody – ISME

Plant, root, and soil microbiome

Preprint: Maize residues changes soil fungal composition and decrease soil microbial co-ocurrence networks complexity – Cobo-Diaz – BioRxiv

Water and extremophile microbiome

Impacts of continuous inflow of low concentrations of silver nanoparticles on biological performance and microbial communities of aerobic heterotrophic wastewater biofilm – Alizadeh – Journal of Agricultural and Food Chemistry

Phages and viruses

Preprint: Metagenomic exploration of viral diversity and virus-host interactions in a deep freshwater lake – Okazaki – BioRxiv

Preprint: Identification and evolution of avian endogenous foamy viruses – Chen – BioRxiv

Viral Diversity of Tick Species Parasitizing Cattle and Dogs in Trinidad and Tobago – Sameroff – Scientific Reports

Bioinformatics

Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences – Mallick – Nature Communications

Heterogeneity spacers in 16S rDNA primers improve analysis of mouse gut microbiomes via greater nucleotide diversity – Jensen – BioTechniques