Author Archives: JP Cardenas

September 22, 2024

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Human and General Microbiome

Multi-way modelling of oral microbial dynamics and host-microbiome interactions during induced gingivitis – G R van der Ploeg – NPJ Biofilms and Microbiomes

Establishing human microbial observatory programs in low- and middle-income countries – Jeffrey I Gordon – Annals of the New York Academy of Sciences

Vaginal microbiota stability over 18 months in young student women in France – Jeanne Tamarelle – European Journal of Clinical Microbiology & Infectious Diseases

Transfer and persistence of microbiota markers from the human hand to the knife: A preliminary study – Sukriye Karadayı – Journal of Forensic and Legal Medicine

Dental Caries: The Way Forward – D T Kopycka-Kedzierawski – JDR Clinical and Translational Research

Changes in the Firmicutes to Bacteriodetes ratio in the gut microbiome in individuals with anorexia nervosa following inpatient treatment: A systematic review and a case series – Passent Helal – Brain and Behavior

Fusobacterium nucleatum facilitates anti-PD-1 therapy in microsatellite stable colorectal cancer – Xueliang Wang – Cancer Cell

Bacterial Extracellular Vesicles as Potential Promoting Factors for Oral Lichen Planus Pathogenesis – Yu Gyung Kim – Inflammation

Gut microbiota metabolite trimethylamine N-oxide promoted NAFLD progression by exacerbating intestinal barrier disruption and intrahepatic cellular imbalance – Fulin Nian – International Immunopharmacology

Comment: Strengthening the foundation of African microbiome research: strategies for standardized data collection – Soumaya Kouidhi – Nature Reviews: Gastroenterology & Hepatology

Review: Microbiota-gut-brain axis in health and neurological disease: Interactions between gut microbiota and the nervous system – Yuhong He – Journal of Cellular and Molecular Medicine

Review: Effect of Staphylococcus aureus colonization and immune defects on the pathogenesis of atopic dermatitis – Evrim Özdemіr – Archives of Microbiology

Beneficial Microbes and Compounds

Gastrointestinal Self-Adaptive and Nutrient Self-Sufficient Akkermansia muciniphila-Gelatin Porous Microgels for Synergistic Therapy of Ulcerative Colitis – Yujie Zhang – ACS Nano

2′-Fucosyllactose attenuates aging-related metabolic disorders through modulating gut microbiome-T cell axis – Ang Li – Aging Cell

Review: Akkermansia in the gastrointestinal tract as a modifier of human health – Maria E Panzetta – Gut Microbes

Animal Microbiome (including Animal Models)

Dipeptide metabolite, glutamyl-glutamate mediates microbe-host interaction to boost spermatogenesis – Balázs Juhász – Scientific Reports

Intestinal deguelin drives resistance to acetaminophen-induced hepatotoxicity in female mice – Shenhai Gong – Gut Microbes

Metformin reprograms tryptophan metabolism via gut Microbiome-Derived bile acid metabolites to ameliorate Depression-Like behaviors in mice – Xiaoxian Xie – Brain, Behavior, and Immunity

Food Microbiome

Dynamics of the microbiome and volatile organic compounds during fermentation and aging of soy sauce – Yuichi Mizuno – Journal of Bioscience and Bioengineering

Unveiling the Brazilian kefir microbiome: discovery of a novel Lactobacillus kefiranofaciens (LkefirU) genome and in silico prospection of bioactive peptides with potential anti-Alzheimer properties – Matheus H Silva – BMC Genomics

Plant Microbiome

Pseudomonas fluorescens Inoculation Enhances Salix matsudana Growth by Modifying Phyllosphere Microbiomes, Surpassing Nitrogen Fertilization – Qing Li – Plant, cell & Environment

Environmental Microbiome

Deep insights into the assembly mechanisms, co-occurrence patterns, and functional roles of microbial community in wastewater treatment plants – Zi-Yan Wei – Environmental Research

Genomic profiling of Antarctic geothermal microbiomes using long-read, Hi-C, and single-cell techniques – Nu Ri Myeong – Scientific Data

Septiembre 15, 2024

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Human and General Microbiome

Correlation of gut microbial diversity to sight-threatening diabetic retinopathy – Rehana Khan – BMC Microbiology

Multiomics reveals microbial metabolites as key actors in intestinal fibrosis in Crohn’s disease – Xuehua Li – EMBO Molecular Medicine

Inflammation mediated by gut microbiome alterations promotes lung cancer development and an immunosuppressed tumor microenvironment – Zahraa Rahal – Cancer Immunology Research

Microbial interactions impact stress tolerance in a model oral community – Gina R Lewin – Microbiology Spectrum

The use of metagenomic and untargeted metabolomics in the analysis of the effects of the Lycium barbarum glycopeptide on allergic airway inflammation induced by Artemesia annua pollen – Min Bai – Journal of Ethnopharmacology

Enteric-coated cerium dioxide nanoparticles for effective inflammatory bowel disease treatment by regulating the redox balance and gut microbiome – Yubiao Huang – Biomaterials

Review: Micro- and nano-plastics, intestinal inflammation, and inflammatory bowel disease: A review of the literature – Manasi Agrawal – The Science of the Total Environment

Commentary:  The 3 Ds: Depression, Dysbiosis, and Clostridiodes difficile – Antoine Boustany – Advances in Therapy

Research Highlight: Targeting fatty acid metabolism promotes a healthy vaginal microbiome – Iris Marchal – Nature Biotechnology

Animal Microbiome

Metagenomic analysis of the gut microbiota of hooded cranes (Grus monacha) on the Izumi plain in Japan – Kosuke Takada – FEBS Open Bio

From Skin to Gut: Understanding Microbial Diversity in Rana amurensis and R. dybowskii – Ming-He Yang – Current Microbiology

Plant and Soil Microbiome

Ridge planting increases the rhizosphere microbiome diversity and improves the yield of Pinellia ternata (Thunb.) Breit in North China – Yaofa Li – PloS One

Microbiome Analysis

Forum: Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities – Nicholas A Bokulich – Trends in Microbiology

September 8, 2024

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Human and General Microbiome

Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes – Aarthi Ravikrishnan – Nature Communications

Integrated analysis of facial microbiome and skin physio-optical properties unveils cutotype-dependent aging effects – Chuqing Sun – Microbiome

Regulation of Bacteroides acidifaciens by the aryl hydrocarbon receptor in IL-22-producing immune cells has sex-dependent consequential impact on colitis – Chandani Mitchell – Frontiers in Immunology

The role of KLF5 in gut microbiota and lung adenocarcinoma: unveiling programmed cell death pathways and prognostic biomarkers – Qingliang Fang – Discover Oncology

Healthy first-degree relatives from multiplex families versus simplex families have a higher subclinical intestinal inflammation, a distinct fecal microbial signature, and harbor a higher risk of developing Crohn’s disease – Pablo A Olivera – Gastroenterology

Reversions mask the contribution of adaptive evolution in microbiomes – Paul A Torrillo – eLife

Review: The hidden base of the iceberg: gut peptidoglycome dynamics is foundational to its influence on the host – Richard Wheeler – Gut Microbes

Review: Benefits and concerns of probiotics: an overview of the potential genotoxicity of the colibactin-producing Escherichia coli Nissle 1917 strain – Luca Falzone – Gut Microbes

Book Chapter: Microbial Extracellular Vesicles in Host-Microbiota Interactions – Sarah Abubaker – Results and Problems in Cell Differentiation

Beneficial Microbes and Compounds

A probiotic Limosilactobacillus fermentum GR-3 mitigates colitis-associated tumorigenesis in mice via modulating gut microbiome – Tuoyu Zhou – NPJ Science of Food

Review: Pathophysiological and Clinical Potential of Human Microbiome: Microbe-based Therapeutic Insights – Somali Sanyal – Current Pharmaceutical Biotechnology

Plant Microbiome

Soil volatilomics uncovers tight linkage between soybean presence and soil omics profiles in agricultural fields – Hikari Kuchikata – Scientific Report

Review: Meddling with the microbiota: Fungal tricks to infect plant hosts – Fantin Mesny – Current Opinion in Plant Biology

Environmental Microbiome

A comprehensive catalog encompassing 1376 species-level genomes reveals the core community and functional diversity of anammox microbiota – Depeng Wang – Water Research

Revealing the intricate temporal dynamics and adaptive responses of prokaryotic and eukaryotic microbes in the coastal South China Sea – Wenqian Xu – The Science of the Total Environment

Biodegradation of low-density polyethylene by mixed fungi composed of Alternaria sp. and Trametes sp. isolated from landfill sites – Wei-Kang Yang – BMC Microbiology

Using patterns of shared taxa to infer bacterial dispersal in human living environment in urban and rural areas – M Grönroos – Applied and Environmental Microbiology

Annotation-free prediction of microbial dioxygen utilization – Avi I Flamholz – mSystem

Microbiome Analysis: Tools, Techniques and Resources

MRGM: an enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes – Nayeon Kim – Gut Microbes

A unified web cloud computing platform MiMedSurv for microbiome causal mediation analysis with survival responses – Hyojung Jang – Scientific Reports

A quantitative approach to measure and predict microbiome response to antibiotics – Vincent Tu – mSphere

Metagenomic functional profiling: to sketch or not to sketch? – Mahmudur Rahman Hera – Bioinformatics

TolRad, a model for predicting radiation tolerance using Pfam annotations, identifies novel radiosensitive bacterial species from reference genomes and MAGs – Philip Sweet – Microbiology Spectrum

Review: Improving viral annotation with artificial intelligence – Zachary N Flamholz – mBio

Additionally, the Cold Spring Harbor Protocols Journal released a set of protocols covering the study of Maize Microbiome:

Sampling the Maize (Zea mays) Leaf Microbiome – Jason G Wallace – Cold Spring Harbor Protocols

Sampling Root-Associated Microbiome Communities of Maize (Zea mays) – Alonso Favela – Cold Spring Harbor Protocols

Sampling and Analysis of the Maize Microbiome – Jason G Wallace – Cold Spring Harbor Protocols

Manipulating the Maize (Zea mays) Microbiome – Sierra S Raglin – Cold Spring Harbor Protocols

August 18, 2024

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Human and General Microbiome

Maternal antibiotic prophylaxis during cesarean section has a limited impact on the infant gut microbiome – Trishla Sinha – Cell Host & Microbe

Microbial assimilatory sulfate reduction-mediated H(2)S: an overlooked role in Crohn’s disease development – Wanrong Luo – Microbiome (BMC)

Characterization of the vaginal microbiota in Italian women with endometriosis: preliminary study – Rosa Sessa – Archives of Gynecology and Obstetrics

Profiles and interactions of gut microbiome and intestinal microRNAs in pediatric Crohn’s disease – Yao Lv – mSystems

Regional variation and adaptive evolution in Bifidobacterium pseudocatenulatum: Insights into genomic and functional diversity in human gut – Qiong Wu – Food Research International

Review: Effects of physical exercise on Akkermansia muciniphila: a systematic review of human and animal studies – S S Aguiar – Beneficial Microbes

Beneficial Microbes and Compounds

Commentary: Microbiome modification for personalized treatment of dysbiotic diseases – R Balfour Sartor – Cell Host & Microbe

Combining Gut Microbiota Modulation and Enzymatic-Triggered Colonic Delivery by Prebiotic Nanoparticles Improves Mouse Colitis Therapy – Hui Li – Biomaterials Research

Animal Microbiome

Effect of chronic alcohol consumption on oral microbiota in rats with periodontitis – Zirui Zhao – PeerJ

Fecal microbiota transplantation accelerates restoration of florfenicol-disturbed intestinal microbiota in a fish model – Zhuoran Han – Communications Biology

Structural, Biochemical, and Phylogenetic Analysis of Bacterial and Fungal Carbohydrate Esterase Family 15 Glucuronoyl Esterases in the Rumen – Robert J Gruninger – The Protein Journal

Plant Microbiome

Review: Harnessing the plant microbiome for sustainable crop production – Stéphane Compant – Nature Reviews Microbiology

Review: The impact of filamentous plant pathogens on the host microbiota – Victor M Flores-Nunez – BMC Biology

Environmental Microbiome

Metagenomic insights into the prokaryotic communities of heavy metal-contaminated hypersaline soils – Cristina Galisteo – The Science of the Total Environment

Ecological phage therapy: Can bacteriophages help rapidly restore the soil microbiome? – Tarryn Davies – Ecology and Evolution

Do restoration strategies in mangroves recover microbial diversity? A case study in the Yucatan peninsula – Daniel Esguerra-Rodríguez – PloS One

Metagenome sequencing and 107 microbial genomes from seamount sediments along the Yap and Mariana trenches – Yue Zhang – Scientific Data

Microbiome Analysis: Tools, Techniques and Resources

Metrological evaluation of DNA extraction method effects on the bacterial microbiome and resistome in sputum – Aleksander Benčič – mSystems

Commentary: AI in microbiome research: Where have we been, where are we going? – Georg K Gerber – Cell Host & Microbe

Review: Modeling Microbial Communities: Perspective and Challenges – Lavanya Raajaraam – ACS Synthetic Biology

August 11, 2024

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Human and General Microbiome

B cell senescence promotes age-related changes in oral microbiota – Hiroya Mizuno – Aging Cell

Exploring the relationship between gut microbiota and breast cancer risk in European and East Asian populations using Mendelian randomization – Wei Lin – BMC Cancer

Intratumoral microbiome promotes liver metastasis and dampens adjuvant imatinib treatment in gastrointestinal stromal tumor – Yanze Li – Cancer Letters

Comparison of Vaginal microbiota in HPV-negative and HPV-positive pregnant women using a culture-based approach – Podoprigora Irina – Diagnostic Microbiology and Infectious Disease

The gut-microbiome in adult Attention-deficit/hyperactivity disorder – A Meta-analysis – Babette Jakobi – European Neuropsychopharmacology

An Empirical Dietary Pattern Associated with the Gut Microbial Features in Relation to Colorectal Cancer Risk – Kai Wang – Gastroenterology

Species-level characterization of gut microbiota and their metabolic role in kidney stone formation using full-length 16S rRNA sequencing – Bashir Hussain – Urolithiasis

Review: Game of microbes: the battle within – gut microbiota and multiple sclerosis – Ti-Ara Turner – Gut Microbes

Review: The early life exposome and autism risk: a role for the maternal microbiome? – Claudia M Di Gesù – Gut Microbes

Review: Gut mycobiome alterations and implications for liver diseases – Suling Zeng – PLoS Pathogens

Beneficial Microbes and Compounds

A novel intervention of molecular hydrogen on the unbalance of the gut microbiome in opioid addiction: Experimental and human studies – Bing Xie – Biomedicine & Pharmacotherapy

Lower fecal microbiota transplantation ameliorates ulcerative colitis by eliminating oral-derived Fusobacterium nucleatum and virulence factor – Dong-Hao Li – Gut Pathogens

Induction of Cell Death by Bifidobacterium infantis DS1685 in Colorectal and Breast Cancers via SMAD4/TGF-Beta Activation – In Hwan Tae – Journal of Microbiology and Biotechnology

Review: Peptide GLP-1 receptor agonists: From injection to oral delivery strategies – Zhiqiang Ke – Biochemical Pharmacology

Animal Microbiome (including model experiments)

Stress-sensitive neural circuits change the gut microbiome via duodenal glands – Hao Chang – Cell

Effect of Hafnia alvei on Morphophysiologic Parameters and Gut Microbiota of Mice with Inherited Type 2 Diabetes Mellitus – V A Zolotarev – Bulletin of Experimental Biology and Medicine

Spatial analysis of murine microbiota and bile acid metabolism during amoxicillin treatment – Chapman N Beekman – Cell Reports

Evaluating impacts of radiation-induced sterilization on the performance and gut microbiome of mass-reared Mediterranean fruit fly (Ceratitis capitata) in Hawai’i – Charles J Mason – Journal of Economic Entomology

Plant Microbiome

Disease Resistance Correlates with Core Microbiome Diversity in Cotton – Rhea Aqueel – Current Microbiology

Environmental Microbiome

The symbiotic alga Trebouxia fuels a coherent soil ecosystem on the landscape scale in the Atacama Desert – Patrick Jung – Environmental Microbiome

Relationships between radiation, wildfire and the soil microbial communities in the Chornobyl Exclusion Zone – Alexandre Barretto de Menezes – The Science of the Total Environment

The first large scale rDNA amplicon database of soil microbiomes from Pamir Plateau, China – Jing Zhu – Scientific Data

Food and Beverage Microbiome

Changes in the solid-associated bacterial and fungal communities following ruminal in vitro fermentation of winery by-products: aspects of the bioactive compounds and feed safety – Ratchaneewan Khiaosa-Ard – Anaerobe

16S amplicon-based microbiome biomapping of a commercial broiler hatchery – Michael J Jr Rothrock – Animal Microbiome

Analyzing the gut microbiota and microbial-associated metabolites of tomato-based sauces – Alicia Paulina Cárdenas-Castro – Food Chemistry

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

July 28, 2024

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Human and General Microbiome

Shaping Microbiota During the First 1000 Days of Life – Anna Samarra – Advances in Experimental Medicine and Biology

Role of sulfidogenic members of the gut microbiota in human disease – Andreia I Pimenta – Advances in Microbial Physiology

Fecal microbiota transplantation improves anti-PD-1 inhibitor efficacy in unresectable or metastatic solid cancers refractory to anti-PD-1 inhibitor – Yunjae Kim – Cell Host & Microbe

Exploring the genomic traits of infant-associated microbiota members from a Zimbabwean cohort – Taona Emmah Mudhluli – BMC Genomics

Gut microbial features and circulating metabolomic signatures of frailty in older adults – Yanni Pu – Nature Aging

Gut microbiome and metabolome signatures in liver cirrhosis-related complications – Satya Priya Sharma – Clinical and Molecular Hepatology

Detection of Microplastics in Human Breast Milk and Its Association with Changes in Human Milk Bacterial Microbiota – Apisith Saraluck – Journal of Clinical Medicine

Regional Differences in Microbial Infiltration of Brain Tissue from Alzheimer’s Disease Patients and Control Individuals – T Bucky Jones – Brain Sciences

Review: Aggregatibacter actinomycetemcomitans: From the Oral Cavity to the Heart Valves – Jasminka Talapko – Microorganisms

Beneficial Microbes and Compounds

Review: Digesting the complex metabolic effects of diet on the host and microbiome – Rachel N Carmody – Cell

Review: A comprehensive review of synbiotics: an emerging paradigm in health promotion and disease management – Sulhee Lee – World Journal of Microbiology & Biotechnology

Animal Model Microbiome

Desulfovibrio vulgaris caused gut inflammation and aggravated DSS-induced colitis in C57BL/6 mice model – Guoxin Huang – Gut Pathogens

LCN2 regulates the gut microbiota and metabolic profile in mice infected with Mycobacterium bovis – Quntao Huang – mSystems

Non-Model Animal Microbiome

Multiomics of parkinsonism cynomolgus monkeys highlights significance of metabolites in interaction between host and microbiota – Jiang-Mei Gao – NPJ Biofilms and Microbiomes

Vaginal and Uterine Microbiota of Healthy Maiden Mares during Estrus – Ana Gil-Miranda – Veterinary Sciences

Review: Reproductive Tract Microbiota of Mares – Ana Gil-Miranda – Veterinary Sciences

Environmental Microbiology

Soils of two Antarctic Dry Valleys exhibit unique microbial community structures in response to similar environmental disturbances – Mafalda S Baptista – Environmental Microbiome

Plant Microbiome

Thermal sensitivity of soil microbial carbon use efficiency across forest biomes – Chengjie Ren – Nature Communications

Miscanthus sp. root exudate alters rhizosphere microbial community to drive soil aggregation for heavy metal immobilization – Bohan Wu – The Science of the Total Environment

Soil conditions modify species diversity effects on tree functional trait expression – Andréa Davrinche – Scientific Reports

Microbiome Analysis

A novel system to culture human intestinal organoids under physiological oxygen content to study microbial-host interaction – Tatiana Y Fofanova – PloS ONE

Compositional Data and Microbiota Analysis: Imagination and Reality – Tatsuki Itagaki – Microorganisms

Thanos: An R Package for the Gene-Centric Analysis of Functional Potential in Metagenomic Samples – Zhe Zhao – Microorganisms

July 21, 2024

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Human and General Microbiome

Akkermansia muciniphila and Parabacteroides distasonis as prognostic markers for relapse in ulcerative colitis patients – Ana Mendes-Frias – Frontiers in Cellular and Infection Microbiology

Obesity-enriched gut microbe degrades myo-inositol and promotes lipid absorption – Chao Wu – Cell Host & Microbe

Gut microbiome in endometriosis: a cohort study on 1000 individuals – Inmaculada Pérez-Prieto – BMC Medicine

Metagenomic analysis reveals altered gut virome and diagnostic potential in pancreatic cancer – Pan Zhang – Journal of Medical Virology

The tumor microbiome as a predictor of outcomes in patients with metastatic melanoma treated with immune checkpoint inhibitors – Caroline E Dravillas – Cancer Research Communications

Gut microbiome diversity within Clostridia is negatively associated with human obesity – Laura Salazar-Jaramillo – mSystems

Early depletion of gut microbiota shape oligodendrocyte response after traumatic brain injury – Kirill Shumilov – Journal of Neuroinflammation

Effect of progestin-based contraceptives on HIV-associated vaginal immune biomarkers and microbiome in adolescent girls – Mélodie A Nasr – PloS One

Review: Microbiome and pancreatic cancer: time to think about chemotherapy – Juliana de Castilhos – Gut Microbes

Review: Host control of the microbiome: Mechanisms, evolution, and disease – Jacob Wilde – Science

Review: Connecting microbial community assembly and function – Leonora S Bittleston – Current Opinion in Microbiology

Review: Microbiota of Saliva: A Non-invasive Diagnostic Tool – Dasharath B Shinde – Indian Journal of Microbiology

Beneficial Microbes, Compounds and Interventions

Topical prebiotic nitrate: optimizing the ‘hang-time’, source and dose for specific oral or systemic effects – Bob T Rosier – NPJ Biofilms and Microbiomes

An improved diet-based nutritional interventions can improve childhood obesity with the synergistic regulation of gut microbiota – M Zhou – Beneficial Microbes

Intermittent fasting, calorie restriction, and a ketogenic diet improve mitochondrial function by reducing lipopolysaccharide signaling in monocytes during obesity: A randomized clinical trial – Martha Guevara-Cruz – Clinical Nutrition 

Food Microbiome

Influence of the initial microbiota on eggplant shibazuke pickle and eggplant juice fermentation – Kazunori Sawada – Microbiology Spectrum

Metatranscriptomics reveals microbial community function succession and characteristic flavor formation mechanisms during black rice wine fermentation – Aoxing Tang – Food Chemistry

Animal Model Microbiome

Gα13 restricts nutrient driven proliferation in mucosal germinal centers – Hang T Nguyen – Nature Immunology

Gut microbiota mediates ambient PM(2.5) exposure-induced abnormal glucose metabolism via short-chain fatty acids – Wenpu Shao – Journal of Hazardous Materials

Non-Model Animal Microbiome

Domestication and evolutionary histories of specialized gut symbionts across cephalotine ants – Christian Cabuslay – Molecular Ecology

Review: The interplay between gut symbionts and behavioral variation in social insects – Joanito Liberti – Current Opinion in Insect Science

Meta-transcriptomic analysis of companion animal infectomes reveals their diversity and potential roles in animal and human disease – Wei-Chen Wu – mSphere

Alcohol consumption during pregnancy differentially affects the fecal microbiota of dams and offspring – Tamara S Bodnar – Scientific Reports

Environmental Microbiome

Meta-omics analysis reveals the marine arsenic cycle driven by bacteria – Zhao-Jie Teng – Journal of Hazardous Materials

Using Machine Learning to Identify Environmental Factors that Collectively Determine Microbial Community Structure of Activated Sludge – Lu Wang – Environmental Research

Microplastic pollution promotes soil respiration: A global-scale meta-analysis – Shuling Zhao – Global Change Biology

SMMP: A Deep-Coverage Marine Metaproteome Method for Microbial Community Analysis throughout the Water Column Using 1 L of Seawater – Songduo Wang – Analytical Chemistry

Metagenomic insights into microbial community structure and metabolism in alpine permafrost on the Tibetan Plateau – Luyao Kang – Nature Communications

Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass – Xuejiao Lyu – Journal of Industrial Microbiology & Biotechnology

Microbiome Analysis

GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs – Jianshu Zhao – Nucleic Acids Research

Multi-omics machine learning to study host-microbiome interactions in early-onset colorectal cancer – Thejus T Jayakrishnan – NPJ Precision Oncology

3D printed rectal swabs for assessing the gut microbiome, metabolome and inflammation – Robert W Perry – Scientific Reports

AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides – Amin Darabi – BMC Bioinformatics

JASPER: Fast, powerful, multitrait association testing in structured samples gives insight on pleiotropy in gene expression – Joelle Mbatchou – American Journal of Human Genetics

Microbial Evolution

The nature of the last universal common ancestor and its impact on the early Earth system – Edmund R R Moody – Nature Ecology & Evolution

July 7, 2024

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Human and General Microbiome

Changes in the gut microbiome of patients with esophageal cancer: a systematic review and meta-analysis based on 16S gene sequencing technology – Jieyin Deng – Microbial Pathogenesis

Integrated metagenomic and metabolomic analysis reveals distinctive stage-specific gut-microbiome-derived metabolites in intracranial aneurysms – Haitao Sun – Gut

After surgically induced remission, ileal and colonic mucosa-associated microbiota predicts Crohn’s disease recurrence – Cristian-Hernandez Rocha – Clinical Gastroenterology and Hepatology

Human gut microbiota analysis of cystic fibrosis infants using metaproteomics – C García-Durán – Microbiology Resource Announcements

Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages – Shivkumar Vishnempet Shridhar – Cell Reports

Perturbations in gut microbiota composition in schizophrenia – YiMeng Wang – PloS One

Maternal gestational diabetes mellitus associates with altered gut microbiome composition and head circumference abnormalities in male offspring – Shilan Wang – Cell host & Microbe

Microbial signatures and continuum in endometrial cancer and benign patients – Anita Semertzidou – Microbiome

Comparison of shipping versus immediate freezer storage of vaginal samples for vaginal microbiota assessment – Susan Tuddenham – Sexually Transmitted Infections

Letter: Real-world bisphenol A exposure not linked to microbiota dynamics in childhood obesity – Robyn L Prueitt – mSystems

Essay: Blockbuster T cells in the gut: A high-resolution view of immune modulation by the gut microbiome is presented – Kazuki Nagashima – Science

Review: Gut microbiota-lncRNA/circRNA crosstalk: implications for different diseases – Lei Zhang – Critical Reviews in Microbiology

Review: The role of gut microbiota, exosomes, and their interaction in the pathogenesis of ALD – Zilu Cheng – Journal of Advanced Research

Review: Integrating host and microbiome biology using holo-omics – Carl M Kobel – Molecular Omics

Beneficial Microbes, Compounds, and Interventions

Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments – Torben Sølbeck Rasmussen – Microbiome

Fecal microbiota transplantation alters gut phage communities in a clinical trial for obesity – Michele Zuppi – Microbiome

A meta-analysis of randomized controlled trials evaluating the effectiveness of fecal microbiota transplantation for patients with irritable bowel syndrome – Yu Wang – BMC Gastroenterology

Faecalibaterium prausnitzii strain EXL01 boosts efficacy of immune checkpoint inhibitors – Marius Bredon – Oncoimmunology

Serum and CSF metabolomics analysis shows Mediterranean Ketogenic Diet mitigates risk factors of Alzheimer’s disease – Annalise Schweickart – NPJ Metabolic Health and Disease

Oral histidine affects gut microbiota and MAIT cells improving glycemic control in type 2 diabetes patients – Moritz V Warmbrunn – Gut Microbes

The Evolution of Science and Regulation of Dietary Supplements: Past, Present, and Future – Paul M Coates – The Journal of Nutrition

Review: Dietary patterns interfere with gut microbiota to combat obesity – Xiaofan Lou – Frontiers in Nutrition

Plant Microbiome

Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health – Sang-Moo Lee – The ISME Journal

Review: Unearthing the power of microbes as plant microbiome for sustainable agriculture – Arpan Mukherjee – Microbiological Research

Review: Surviving the Stress: Understanding the Molecular Basis of Plant Adaptations and Uncovering the Role of Mycorrhizal Association in Plant Abiotic Stresses – Vivek Sharma – Microbial Pathogenesis

Environmental Microbiome

The drainome: longitudinal metagenomic characterisation of wastewater from hospital ward sinks to characterize the microbiome and resistome and assess the effects of decontamination interventions – Luke B Snell – The Journal of Hospital Infection

Review: Beyond Meta-Omics: Functional Genomics in Future Marine Microbiome Research – Yin Chen – Annual Review of Marine Science

Review: Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges – Haixia Pan – Current Microbiology

Forensic Microbiome

16S rRNA, metagenomics and 2bRAD-M sequencing to decode human thanatomicrobiome – Xin Huang – Scientific Data

Microbiome Analysis

A graph neural network approach for predicting drug susceptibility in the human microbiome – Maryam – Computers in Biology and Medicine

Protocol for the construction and functional profiling of metagenome-assembled genomes for microbiome analyses – Goutam Banerjee – STAR Protocols

DeepPIG: deep neural network architecture with pairwise connected layers and stochastic gates using knockoff frameworks for feature selection – Euiyoung Oh – Scientific Reports

CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets – Orges Koci – Microbiome

June 30, 2024

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Human and General Microbiome

Gut

Metaproteomic portrait of the healthy human gut microbiota – Alessandro Tanca – NPJ Biofilms and Microbiomes

Microbiome and Growth in Infants with Congenital Heart Disease – Michael P Fundora – The Journal of Pediatrics

Driving gut microbiota enterotypes through host genetics – Catherine Larzul – Microbiome

Obesity-associated microbiomes instigate visceral adipose tissue inflammation by recruitment of distinct neutrophils – Dharti Shantaram – Nature Communications

Fecal, Duodenal and Tumor Microbiota Composition of Esophageal Carcinoma Patients, a Longitudinal Prospective Cohort – Tom van den Ende – Journal of the National Cancer Institute

Review: Role of the intestinal microbiota in contributing to weight disorders and associated comorbidities – Matthias Van Hul – Clinical Microbiology Reviews

Review: The role of the gut microbiome in disorders of gut-brain interaction – Brent J Gawey – The FEBS Journal

Skin

Multi-omics signatures reveal genomic and functional heterogeneity of Cutibacterium acnes in normal and diseased skin – Tianze Yu – Cell Host & Microbe

Genitourinary Tract

Vaginal anaerobes are associated with cervicitis: a case-control study – Erica L Plummer – The Journal of Infection

Oral and Respiratory Tract

Review: The Impact of Oral Diseases on Respiratory Health and the Influence of Respiratory Infections on the Oral Microbiome – Annapurna Gupta – Journal of Dentistry

Beneficial Microbes and Compounds

Lactobacillus acidophilus protects against Corynebacterium pseudotuberculosis infection by regulating the autophagy of macrophages and maintaining gut microbiota homeostasis in C57BL/6 mice – Dengliang Li – mSystems

Exploring novel microbial metabolites and drugs for inhibiting Clostridioides difficile – Ahmed A Abouelkhair – mSphere

Ketogenic diet-induced bile acids protect against obesity through reduced calorie absorption – Xiao Li – Nature Metabolism

Review: How Diet and Lifestyle Can Fine-Tune Gut Microbiomes for Healthy Aging – M Tamayo – Annual Review of Food Science and Technology

Animal Microbiome

Gut microbiota signatures of vulnerability to food addiction in mice and humans – Solveiga Samulėnaitė – Gut

Group membership, not diet, structures the composition and functional potential of the gut microbiome in a wild primate – Peter M Finnegan – mSphere

Maternal transmission as a microbial symbiont sieve, and the absence of lactation in male mammals – Brennen T Fagan – Nature Communications

Built Environment Microbiome

A metagenomic assessment of bacterial community in spices sold open-air markets in Saint-Louis, Senegal – Sarbanding Sané – Scientific Reports

Microbiome Analysis: Tools, Techniques and Resources

Compositionally aware estimation of cross-correlations for microbiome data – Ib Thorsgaard Jensen – PloS ONE

Bioinformatic Workflows for Metaproteomics – Tanja Holstein – Methods in Molecular Biology 

Floria: fast and accurate strain haplotyping in metagenomes – Jim Shaw – Bioinformatics 

Enhancing antimicrobial resistance detection with MetaGeneMiner: Targeted gene extraction from metagenomes – Chang Liu – Chinese Medical Journal

Benchmarking low- and high-throughput protein cleanup and digestion methods for human fecal metaproteomics – Alessandro Tanca – mSystems

Genome Watch: Bacterial barcoding facilitates plant microbiome studies – Hualan Liu – Nature Reviews Microbiology

Other

Retraction Note: Microbiome analyses of blood and tissues suggest cancer diagnostic approach – Gregory D Poore – Nature