Tag Archives: Beneficial Microbes and Compounds

August 4, 2024

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Human Gut Microbiome

Exploring the interplay between antiretroviral therapy and the gut-oral microbiome axis in people living with HIV – Aswathy Narayanan – Scientific Reports

Human Gut Microbiota Composition Associated with International Travels – D Henares – Travel Medicine and Infectious Disease

Respiratory microbiome and clinical course of carbapenem-resistant Acinetobacter baumannii pneumonia in critically Ill patients – Jin Gu Yoon – Medicine

Review: Gut Microbiota and Autism Spectrum Disorder: A Neuroinflammatory Mediated Mechanism of Pathogenesis? – Fatemeh Zarimeidani – Inflammation

Review: Gut microbiota and eating behaviour in circadian syndrome – Jorge R Soliz-Rueda – Trends in Endocrinology and Metabolism

Beneficial Microbes and Compounds

Staphylococcus aureus/Staphylococcus epidermidis from skin microbiota are balanced by Pomegranate peel extract: An eco-sustainable approach – Sara D’Arcangelo – PloS One

Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities – Francesca De Filippis – NPJ Biofilms and Microbiomes

Bugs as drugs: Extended clinical applications and potential translational trends of Akkermansia muciniphila in oncology and comprehensive clinical investigation panorama of therapeutic microbiome modulators in gastric cancer treatment – Yuning Wang – Pharmacological Research

Polyphenols: potent protectors against chronic diseases – Geetha Shanmugam – Natural Product Research

Animal Microbiome

Effects of berberine hydrochloride on antioxidant response and gut microflora in the Charybdis japonica infected with Aeromonas hydrophila – Mingming Han – BMC Microbiology

Design of an agro-industrial by-products-based media for the production of probiotic bacteria for fish nutrition – Marcelo Fernando Valle Vargas – Scientific Reports

Association of microbial community structure with gill disease in marine-stage farmed Atlantic salmon (Salmo salar); a yearlong study – Morag Clinton – BMC Veterinary Research

Selection for stress tolerance and longevity in Drosophila melanogaster have strong impacts on microbiome profiles – Torsten Nygaard Kristensen – Scientific Reports

Novel insights on microbiome dynamics during a gill disease outbreak in farmed rainbow trout (Oncorhynchus mykiss) – Samuele Zamparo – Scientific Reports

Gut Microbiome-Driven metabolites influence skin pigmentation in TYRP1 mutant Oujiang color common carp – Roland Nathan Mandal – Gene

Plant and Soil Microbiome

From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology – Winston E Anthony – Environmental Microbiome

An acidophilic fungus promotes prey digestion in a carnivorous plant – Pei-Feng Sun – Nature Microbiology

A novel strategy of artificially regulating plant rhizosphere microbial community to promote plant tolerance to cold stress – Jianfeng Zhang – The Science of the Total Environment

A bud’s life: Metabarcoding analysis to characterise hazelnut big buds microbiome biodiversity – Silvia Turco – Microbiological Research

Perspective: Integrating viruses into soil food web biogeochemistry – Cátia Carreira – Nature Microbiology

Review: Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health – Morgane Duret – Microbiological Research

Environmental Microbiome

Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses – Alexandra K Stiffler – Microbiome

September 4, 2023

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Human and General Microbiome

Gut microbial carbohydrate metabolism contributes to insulin resistance – Tadashi Takeuchi – Nature

Gut Microbiome in Patients With Early-Stage and Late-Stage Melanoma – Russell G Witt – JAMA Dermatology

The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children – A Cristina Paulo – Microbiome

Salivary microbiome of healthy women of reproductive age – Eline Cauwenberghs – mBio

Microbiome characteristics description of COVID-19 patients based on bulk RNA-seq and scRNA-Seq data – Sainan Zhang – Computers in Biology and Medicine

Parkinson’s disease alters the composition of subgingival microbiome – Ekin Yay – Journal of Oral Microbiology

Cervicovaginal Gardnerella sialidase-encoding gene in persistent human papillomavirus infection – Juliano Novak – Scientific Reports

Human milk oligosaccharides modulate the intestinal microbiome of healthy adults – Jonathan P Jacobs – Scientific Reports

Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease – Prabha Chandrasekaran – The Journal of Allergy and Clinical Immunology

Review: The curious case of Prevotella copri – Nehal Adel Abdelsalam – Gut Microbes

Review: Gut microbiota and microbiota-derived metabolites in colorectal cancer: enemy or friend – Xinyi Wang – World Journal of Microbiology & Biotechnology

Beneficial Microbes and Compounds

N-Acetylglucosamine and its dimer ameliorate inflammation in murine colitis by strengthening the gut barrier function – Sung-In Choi – Food & Function

Omega-3 nanoemulgel in prevention of radiation-induced oral mucositis and its associated effect on microbiome: a randomized clinical trial – Basma M Morsy – BMC Oral Health

Lactiplantibacillus plantarum ELF051 Alleviates Antibiotic-Associated Diarrhea by Regulating Intestinal Inflammation and Gut Microbiota – Wei Liang – Probiotics and Antimicrobial Proteins

Animal Microbiome

Microbiomes and metabolomes of dominant coral reef primary producers illustrate a potential role for immunolipids in marine symbioses – Helena Mannochio-Russo – Communications Biology

Alteration of diet microbiota limits the experimentally evolved immune priming response in flour beetles, but not pathogen resistance – Arun Prakash – Journal of Evolutionary Biology

Mammals show distinct functional gut microbiome dynamics to identical series of environmental stressors – Adam Koziol – mBio

Microbiome and Evolution

The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome – Anurag Chaturvedi – Nucleic Acids Research

Review: Impact of intraspecific variation in insect microbiomes on host phenotype and evolution – Claudia Lange – The ISME Journal

Review: Why do hosts malfunction without microbes? Missing benefits versus evolutionary addiction – Tobin J Hammer – Trends in Microbiology

Environmental Microbiome

Different microbial assemblage colonized on microplastics and clay particles in aerobic sludge treatment – Zixuan Zhang – The Science of the Total Environment

More Microbes

Metagenomic insights into the microbiota involved in lactate and butyrate production and manipulating their synthesis in alfalfa silage – Rongrong Li – Journal of Applied Microbiology

Microbiome Research Tools

RSim: A reference-based normalization method via rank similarity – Bo Yuan – PLoS Computational Biology

Review: Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview – Tomasz Boruta – Computational and Structural Biotechnology Journal

Preprint: Analyzing microbial evolution through gene and genome phylogenies – Sarah Teichman – bioRxiv

August 20, 2023

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Highlights!

Human microbiome variation associated with race and ethnicity emerges as early as 3 months of age – Elizabeth K Mallott – PLoS Biology

Mapping the T cell repertoire to a complex gut bacterial community – Kazuki Nagashima – Nature

Comparison of the relative impacts of acute consumption of an inulin-enriched diet, milk kefir or a commercial probiotic product on the human gut microbiome and metabolome – Liam H. Walsh – npj Science of Food 

High-resolution strain-level microbiome composition analysis from short reads – Herui Liao – Microbiome

Preprint: Profiling novel lateral gene transfer events in the human microbiome –  Tiffany Y. Hsu – bioRxiv

Human and General Microbiome

Preprint: Major data analysis errors invalidate cancer microbiome findings –  Abraham Gihawi – bioRxiv

Microdiversity of the vaginal microbiome is associated with preterm birth – Jingqiu Liao – Nature Communications

Dysbiosis of gut microbiota during fecal stream diversion in patients with colorectal cancer – Soo Young Lee – Gut Pathogens

The gut microbiome contributes to somatic morphine withdrawal behavior and implicates a TLR2 mediated mechanism – Bridget Truitt – Gut Microbes

Association of the human gut microbiota with vascular stiffness – Rafael R C Cuadrat – Scientific Reports

Gut microbiota and intervertebral disc degeneration: a bidirectional two-sample Mendelian randomization study – Ziming Geng – Journal of Orthopaedic Surgery and Research

News & Views: Microbiome alterations in autism spectrum disorder – Elena J Coley-O’Rourke – Nature Microbiology

Beneficial Microbes and Compounds

Rosmarinic acid alleviates intestinal inflammatory damage and inhibits endoplasmic reticulum stress and smooth muscle contraction abnormalities in intestinal tissues by regulating gut microbiota – Kan Li – Microbiology Spectrum

Prevotella copri alleviates sarcopenia via attenuating muscle mass loss and function decline – Xiaolei Liu – Journal of Cachexia, Sarcopenia and Muscle

The Influence of Protein Secretomes of Enterococcus durans on ex vivo Human Gut Microbiome – Carolina Baldisserotto Comerlato – Probiotics and Antimicrobial Proteins

Kombucha tea as an anti-hyperglycemic agent in humans with diabetes – a randomized controlled pilot investigation – Chagai Mendelson – Frontiers in Nutrition 

Animal Microbiome

The unique gut microbiome of giant pandas involved in protein metabolism contributes to the host’s dietary adaption to bamboo – Feilong Deng – Microbiome

Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations – M McCauley – Nature Communications

Review: Toward an Integrated Understanding of the Lepidoptera Microbiome – Yongqi Shao – Annual Review of Entomology

Plant Microbiome

Characterization of bacterial community in tobacco leaves at flue-curing and redrying processing stages – Yue Yang – Scientific Reports

Environmental Microbiome

Inter-comparison of marine microbiome sampling protocols – Francisco Pascoal – ISME Communications

Discovery of a novel bacterial class with the capacity to drive sulfur cycling and microbiome structure in a paleo-ocean analog – Adrien Vigneron – ISME Communications

Microbiome Research: Resources, Tools and Techniques

MT-MAG: Accurate and interpretable machine learning for complete or partial taxonomic assignments of metagenome assembled genomes – Wanxin Li – PloS one

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes – Michael J Pavia – Microbiome

Detection of viable commensal bacteria in murine melanoma tumors by culturomics – Catherine M Phelps – STAR Protocols