September 25, 2023

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Highlights!

Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide – Petros Andrikopoulos – Nature Communications

A blood-based metabolomic signature predictive of risk for pancreatic cancer – Ehsan Irajizad – Cell Reports. Medicine

Enterobacteriaceae growth promotion by intestinal acylcarnitines, a biomarker of dysbiosis in Inflammatory Bowel Disease – Johanna M S Lemons – Cellular and Molecular Gastroenterology and Hepatology

Inducible CRISPR-targeted knockdown of human gut Bacteroides in gnotobiotic mice discloses glycan utilization strategies – Zachary W Beller – PNAS

Review: The gut microbiota and its biogeography – Giselle McCallum – Nature Reviews. Microbiology

Human and General Microbiome

The role of the gut-microbiota-brain axis via the subdiaphragmatic vagus nerve in chronic inflammatory pain and comorbid spatial working memory impairment in complete Freund’s adjuvant mice – Caibao Yue – Journal of Psychiatric Research

Disentangling the interactions between nasopharyngeal and gut microbiome and their involvement in the modulation of COVID-19 infection – Leonardo Mancabelli – Microbiology Spectrum

Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota – Eri Komori – Scientific Reports

Metagenomic sequencing reveals altered gut microbial compositions and gene functions in patients with non-segmental vitiligo – Mei Luan – BMC Microbiology

Review: The role of the glycome in symbiotic host-microbe interactions – Rustam Aminov – Glycobiology

Review: Microbiome-targeted interventions for the control of oral-gut dysbiosis and chronic systemic inflammation – Juan Pacheco-Yanes – Trends in Molecular Medicine

Review: The link between the gut microbiome, inflammation, and Parkinson’s disease – Shiqing Nie – Applied Microbiology and Biotechnology

Food Microbiome

The edible plant microbiome: evidence for the occurrence of fruit and vegetable bacteria in the human gut – Wisnu Adi Wicaksono – Gut Microbes

Animal Microbiome

Reducing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome – N K Newman – Microbiome

Combined effect of a neonicotinoid insecticide and a fungicide on honeybee gut epithelium and microbiota, adult survival, colony strength and foraging preferences – Riccardo Favaro – The Science of the Total Environment

Glyphosate decreases survival, increases fecundity, and alters the microbiome of the natural predator Harmonia axyridis (ladybird beetle) – Xueke Gao – Environmental Research

Unfolding the secrets of microbiome (Symbiodiniaceae and bacteria) in cold-water coral – Sanqiang Gong – Microbiology Spectrum

Combined oral intake of short and long fructans alters the gut microbiota in food allergy model mice and contributes to food allergy prevention – Hideaki Takahashi – BMC Microbiology

Review: The pivotal roles of gut microbiota in insect plant interactions for sustainable pest management – Yuxin Zhang – NPJ Biofilms and Microbiomes

Plant Microbiome

Review: Endophytes Modulate Plant Genes: Present Status and Future Perspectives – Vivek Kumar – Current Microbiology

Environmental Microbiome

Planktonic and epilithic prokaryota community compositions in a large temperate river reflect climate change related seasonal shifts – Attila I Engloner – PloS One

Thiothrix and Sulfurovum genera dominate bacterial mats in Slovak cold sulfur springs – Lea Nosalova – Environmental Microbiome

Built Environment Microbiome

Innovative strategy for the conservation of a millennial mausoleum from biodeterioration through artificial light management – Yuanyuan Bao – NPJ Biofilms and Microbiomes

More Microbes

In vitro and in silico evaluation of the serrapeptase effect on biofilm and amyloids of Pseudomonas aeruginosa – Georgios Katsipis – Applied Microbiology and Biotechnology

Microbiome Analysis: Tools, Techniques and Resources

Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data – Hunyong Cho – Briefings in Bioinformatics

Review: Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data – Ostaizka Aizpurua – Critical Reviews in Biotechnology

September 20, 2023

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General microbiome

Frequency of change determines effectiveness of microbial response strategies – Li et al. – The ISME Journal

Human gut microbiome

Social and psychological adversity are associated with distinct mother and infant gut microbiome variations – Warner et al. – Nature Communications

Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua – Mills et al. – Microbiome

Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts – Hansen et al. – Scientific Reports

The Impacts of Fecal Microbiota Transplantation from Same Sex on the Symptoms of Ulcerative Colitis Patients – Shang et al. – Polish Journal of Microbiology

Animal microbiome (for animals in the wild)

Transcriptomic, 16S ribosomal ribonucleic acid and network pharmacology analyses shed light on the anticoccidial mechanism of green tea polyphenols against Eimeria tenella infection in Wuliangshan black-boned chickens – Song et al. – Parasites & Vectors

Dityrosine Aggravates Hepatic Insulin Resistance in Obese Mice by Altering Gut Microbiota and the LPS/TLR4/NF-κB Inflammatory Pathway – Ding et al. – Molecular Nutrition & Food Research

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

[REVIEW]Microbiome-assisted restoration of degraded marine habitats: a new nature-based solution? – Corinaldesi et al. – Frontiers in Marine Science

Bioinformatics

[PREPRINT]Comparison of computational methods for host removal and classification of mycobacteria from clinical metagenomic data – Hall & Coin – bioRxiv

September 18, 2023

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Human and General Microbiome

Ocular microbiome evaluation in dry eye disease and meibomian gland dysfunction: Values of variables – Davide Borroni – Experimental Eye Research

Regulation of psoriasis, colitis, and the intestinal microbiota by clusterin – Yu Kyung Jun – Scientific Reports

Bridging of host-microbiota tryptophan partitioning by the serotonin pathway in fungal pneumonia – Giorgia Renga – Nature Communications

High-throughput sequencing analysis of the characteristics of the gut microbiota in aged patients with sarcopenia – Yiyi Zhang – Experimental Gerontology

Draft genome sequence of a Fusobacterium nucleatum strain isolated from a patient in Kazakhstan with colorectal cancer – Gulmira Kulmambetova – Microbiology Resource Announcements

Review: The impacts of oral and gut microbiota on alveolar bone loss in periodontitis – Nannan Han – Journal of Periodontal Research

Control of Helicobacter pylori with engineered probiotics secreting selective guided antimicrobial peptides – Ankan Choudhury – Microbiology Spectrum

Animal Microbiome

The synthetic food dye, Red 40, causes DNA damage, causes colonic inflammation, and impacts the microbiome in mice – Qi Zhang – Toxicology Reports

Disruption of the microbiota-gut-brain axis is a defining characteristic of the α-Gal A (-/0) mouse model of Fabry disease – C Delprete – Gut Microbes

Review: Neuroactive metabolites modulated by the gut microbiota in honey bees – Amélie Cabirol – Molecular Microbiology

Microbiome and Evolution

Insights into early evolutionary adaptations of the Akkermansia genus to the vertebrate gut – Dámariz González – Frontiers in Microbiology

Food Microbiome

Review: Microbiome Assembly in Fermented Foods – Nicolas L Louw – Annual Review of Microbiology

Plant Microbiome

Engineering the Maize Root Microbiome: A Rapid MoClo Toolkit and Identification of Potential Bacterial Chassis for Studying Plant-Microbe Interactions – John van Schaik – ACS Synthetic Biology

Environmental Microbiome

Effects of Fe(III) (hydr)oxide mineralogy on the development of microbial communities originating from soil, surface water, groundwater, and aerosols – Yidan Zhang – The Science of the Total Environment

Combination of sequencing batch reactor activated sludge process with sludge lysis using thermophilic bacterial community for minimizing excess sludge – Baoyan Chi – Journal of Environmental Management

September 15, 2023

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Today’s digest features the BugSigDB, AMPSphere and more. Also, you can check out my tips for online conferencing and how to do it better. See you at #MVIF next week!

Respiratory microbiome

The landscape of antibiotic resistance genes in the nasopharynx of preterm infants: Prolonged signature of hospitalization and effects by antibiotics – Achal Dhariwal – bioRxiv

Breast cancer microbiome

Integrating current analyses of the breast cancer microbiome – Sidra Sohail and Michael B. Burns – Plos One

Vaginal microbiome

Diet influences community dynamics following vaginal group B Streptococcus colonization – Christina J. Megli – bioRxiv

Gut microbiome

Gut microbes exacerbate systemic inflammation and behavior disorders in neurologic disease CADASIL – Sheng Liu – Microbiome

Water microbiome

Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean – Mirna Vázquez Rosas Landa – mSystems

Insect microbiome

Plastics shape the black soldier fly larvae gut microbiome and select for biodegrading functions – Francesca De Filippis – Microbiome

Animal experiment

Enhancing Recovery from Gut Microbiome Dysbiosis and Alleviating DSS-Induced Colitis in Mice with a Consortium of Rare Short-Chain Fatty Acid-Producing Bacteria – Achuthan Ambat – bioRxiv

Bioinformatics

BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures – Ludwig Geistlinger – Nature Biotechnology

Computational exploration of the global microbiome for antibiotic discovery – Célio Dias Santos-Júnior – bioRxiv

September 13, 2023

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General microbiome

[Resource]BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures – Geistlinger et al. – Nature Biotechnology

Human oral microbiome

[REVIEW]The oral microbiome: diversity, biogeography and human health – Baker et al. – Nature Reviews Microbiology

Dysbiosis of oral microbiome persists after dental treatment-induced remission of periodontal disease and dental caries – Yama et al. – mSystems

Human nearly-sterile sites (blood, organs, brain)

Proton pump inhibitor treatment aggravates bacterial translocation in patients with advanced cirrhosis and portal hypertension – Sturm et al. – mBio

Human gut microbiome

A faecal metabolite signature of impaired fasting glucose: results from two independent population-based cohorts – Nogal et al. – Diabetes

Composition and functional profiles of gut microbiota reflect the treatment stage, severity, and etiology of acute pancreatitis – Wang et al. – Microbiology Spectrum

Animal microbiome

Langerhans cells shape postnatal oral homeostasis in a mechanical-force-dependent but microbiota and IL17-independent manner – Jaber et al. – Nature Communications

Specific pathway abundances in the neonatal calf faecal microbiome are associated with susceptibility to Cryptosporidium parvum infection: a metagenomic analysis – Hares et al. – Animal Microbiome

Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety – Wortelboer et al. – Nature Communications

Gut microbiota of old mice worsens neurological outcome after brain ischemia via increased valeric acid and IL-17 in the blood – Zeng et al. – Microbiome

Plant, root, and soil microbiome

Different bacterial and fungal community patterns in restored habitats in coal-mining subsidence areas – Wang et al. – Environmental Science and Pollution Research

September 11, 2023

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Human and General Microbiome

Obesity is the main driver of altered gut microbiome functions in the metabolically unhealthy – Jacobo de la Cuesta-Zuluaga – Gut Microbes

Elucidating the Role of the Microbiome in Ocular Diseases – Wendy Luo – The American Journal of Pathology

A binary module for microbiota-mediated regulation of γδ17 cells, hallmarked by microbiota-driven expression of programmed cell death protein 1 – Hsin-I Huang – Cell Reports

Resistant starch decreases intrahepatic triglycerides in patients with NAFLD via gut microbiome alterations – Yueqiong Ni – Cell Metabolism

Microbial signature of plaque and gut in acute coronary syndrome – Eugenia Pisano – Scientific Reports

Impact of the lipase inhibitor orlistat on the human gut microbiota – Yudai Uehira – Obesity Research & Clinical Practice

Metabolic network construction reveals probiotic-specific alterations in the metabolic activity of a synthetic small intestinal community – Jack Jansma – mSystems

Colonic phosphocholine is correlated with Candida tropicalis and promotes diarrhea and pathogen clearance – Xihong Zhou – NPJ Biofilms and Microbiomes

Differential dependence on microbiota of IL-23/IL-22-dependent gene expression between the small- and large-intestinal epithelia – Ayaka Nakatani – Genes to Cells

Identification of microbial markers associated with lung cancer based on multi-cohort 16 s rRNA analyses: A systematic review and meta-analysis – Wenjie Han – Cancer Medicine

Review: Targeting microbial quorum sensing: the next frontier to hinder bacterial driven gastrointestinal infections – Ying Su – Gut Microbes

Review: Illuminating the oral microbiome and its host interactions: recent Advancements in omics and bioinformatics technologies in the context of oral microbiome research – Jonathon L Baker – FEMS Microbiology Reviews

Review: Association between primary Sjögren’s syndrome and gut microbiota disruption: a systematic review and meta-analysis – Yue Shen – Clinical Rheumatology

Beneficial Microbes and Compounds

Washed microbiota transplantation for Clostridioides difficile infection: a national multi-center real-world study – Xia Wu – Journal of Digestive Diseases

Lactobacillus johnsonii N6.2 phospholipids induce immature-like dendritic cells with a migratory-regulatory-like transcriptional signature – Alexandra E Cuaycal – Gut Microbes

Akkermansia muciniphila supplementation prevents cognitive impairment in sleep-deprived mice by modulating microglial engulfment of synapses – Na Li – Gut Microbes

Food Microbiome

Metagenomics and metabolomics of Toddy, an Indian fermented date palm beverage – Souvik Das – Food Research International

Animal Microbiome

Gut microbiota from patients with COVID-19 cause alterations in mice that resemble post-COVID symptoms – Viviani Mendes de Almeida – Gut Microbes

Ingestion and biodegradation of disposable surgical masks by yellow mealworms Tenebrio molitor larvae: Differences in mask layers and effects on the larval gut microbiome – Jiaming Wang – The Science of the Total Environment

Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers – Yu Wang – BMC Genomics

Microbiota-mediated competition between Drosophila species – Antoine Rombaut – Microbiome

Microbial signature profiles of Penaeus vannamei larvae in low-survival hatchery tanks affected by vibriosis – Guillermo Reyes – PeerJ

Fiber deprivation and microbiome-borne curli shift gut bacterial populations and accelerate disease in a mouse model of Parkinson’s disease – Kristopher J Schmit – Cell Reports

Plant Microbiome

Microbial communities associated with resin canal discoloration in mango fruit – Muhammad Umar – Letters in Applied Microbiology

Studying the microbiome of suppressive soils against vascular wilt, caused by Fusarium oxysporum in cape gooseberry (Physalis peruviana) – Daniel Bautista – Environmental Microbiology Reports

Environmental Microbiome

Antarctic snow algae: unraveling the processes underlying microbial community assembly during blooms formation – Daniela F Soto – Microbiome

Understanding how various forms of phosphorus stress affect microbiome functions and boost plant disease resistance: Insights from metagenomic analysis – Jie Kang – The Science of the Total Environment

Reductive soil disinfestation and Fe amendment improve soil microbial composition and Fritillaria production – Yue Yin – Applied Microbiology and Biotechnology

How Benthic Sediment Microbial Communities Respond to Glyphosate and Its Metabolite: a Microcosm Experiment – Christine M Cornish – Microbial Ecology

Functional conservation of microbial communities determines composition predictability in anaerobic digestion – Qiang Lin – The ISME Journal

Microbiome Research Tools

Development of an antibody fused with an antimicrobial peptide targeting Pseudomonas aeruginosa: A new approach to prevent and treat bacterial infections – Kenneth Johnson – PLoS Pathogens

Clustering microbiome data using mixtures of logistic normal multinomial models – Yuan Fang – Scientific Reports

A new spike-in-based method for quantitative metabarcoding of soil fungi and bacteria – Miguel Camacho-Sanchez – International Microbiology

Research Highlight: Microbiome screening platform finds drugs for bugs – Katie Kingwell – Nature Reviews. Drug Discovery

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 28, 2023

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Human and General Microbiome

The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia – Ana Elena Pérez-Cobas – Cell Reports. Medicine

A phenome-wide association study (PheWAS) to identify the health impacts of 4-cresol sulfate in the Nagahama Study – Huiting Ou – Scientific Reports

A meta-analysis of tissue microbial biomarkers for recurrence and metastasis in multiple cancer types – Xuebo Li – Journal of Medical Microbiology 

Microbe Profile: Ruminococcus gnavus: the yin and yang of human gut symbionts – Nathalie Juge – Microbiology

Oral Porphyromonas gingivalis infection affects intestinal microbiota and promotes atherosclerosis – Sowon Park – Journal of Clinical Periodontology

Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: the METS-microbiome study – Gertrude Ecklu-Mensah – Nature Communications

Very early life microbiome and metabolome correlates with primary vaccination variability in children – Michael Shaffer – mSystems

Carbohydrate quality, fecal microbiota and cardiometabolic health in older adults: a cohort study – Alessandro Atzeni – Gut Microbes

Multi-omics analysis revealing the interplay between gut microbiome and the host following opioid use – Udhghatri Kolli – Gut Microbes

The gut microbiota reprograms intestinal lipid metabolism through long noncoding RNA Snhg9 – Yuhao Wang – Science

Staphylococcus epidermidis activates keratinocyte cytokine expression and promotes skin inflammation through the production of phenol-soluble modulins – Michael R Williams – Cell Reports

Review: Targeting nonalcoholic fatty liver disease via gut microbiome-centered therapies – Mijra Koning – Gut Microbes

Review: Intracellular Fusobacterium nucleatum infection increases METTL3-mediated m6A methylation to promote the metastasis of esophageal squamous cell carcinoma – Songhe Guo – Journal of Advanced Research

Beneficial Microbes and Compounds

Characteristics of gut microbiota determine effects of specific probiotics strains in patients with functional constipation – Haohao Zhang – Chinese Medical Journal

Lacticaseibacillus rhamnosus TF318 prevents depressive behavior in rats by inhibiting HPA-axis hyperactivity and upregulating BDNF expression – Yujuan Zhao – Neuroscience Letters

Animal Model Microbiome

Role of mucin glycosylation in the gut microbiota-brain axis of core 3 O-glycan deficient mice – Erika Coletto – Scientific Reports

Non-Model Animal Microbiome

Outer membrane vesicles from a mosquito commensal mediate targeted killing of Plasmodium parasites via the phosphatidylcholine scavenging pathway – Han Gao – Nature Communications

Whole genome analyses of toxicants tolerance genes of Apis mellifera gut-derived Enterococcus faecium strains – Heba A H Zaghloul – BMC Genomics

Fungal Microbiome

The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research – Julia M Kelliher – Microbiome

Plant Microbiome

Microbiome dataset of bacterial and fungal communities in anthosphere of twelve different wild plants in South Korea – Jihoon Kim – Data in Brief 

Environmental and Soil Microbiome

Anthropogenic activities mediate stratification and stability of microbial communities in freshwater sediments – Xiaotian Zhou – Microbiome

Long-term agro-management strategies shape soil bacterial community structure in dryland wheat systems – Shikha Singh – Scientific Reports

Microbial community structure and functional prediction in five full-scale industrial park wastewater treatment plants – Tujun Tong – The Science of the Total Environment

Deterministic Development of Soil Microbial Communities in Disturbed Soils Depends on Microbial Biomass of the Bioinoculum – Yuri Pinheiro Alves de Souza – Microbial Ecology

Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole – Kai Sun – Microbiology Spectrum

A study of microbial diversity in a biofertilizer consortium – Cristóbal Hernández-Álvarez – PloS One

Microbiome Research: Resources, Tools and Techniques

Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data – Aubrey R Odom – Scientific Reports

Amplicon-Based Microbiome Profiling: From Second- to Third-Generation Sequencing for Higher Taxonomic Resolution – Elisabetta Notario – Genes

A flexible quasi-likelihood model for microbiome abundance count data – Yiming Shi – Statistics in Medicine

Identification of multivariable Boolean patterns in microbiome and microbial gene composition data – George Golovko – Bio Systems

Machine learning classification by fitting amplicon sequences to existing OTUs – Courtney R Armour – mSphere

Review: Statistical normalization methods in microbiome data with application to microbiome cancer research – Yinglin Xia – Gut Microbes

Book Chapter: Elucidating the role of microbes in celiac disease through gnotobiotic modeling – Alberto Caminero – Methods in Cell Biology

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

August 13, 2023

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Highlights!

Enterotypes of the human gut mycobiome – Senying Lai – Microbiome

Effect of butyrate-producing enterobacteria on advanced hepatocellular carcinoma treatment with atezolizumab and bevacizumab – Kazuhiro Nouso – Cancer Medicine

Parvimonas micra can translocate from the subgingival sulcus of the human oral cavity to colorectal adenocarcinoma – Kelly Conde-Pérez – Molecular Oncology

An Oral Microbial Biomarker for Early Detection of Recurrence of Oral Squamous Cell Carcinoma – Wei-Ni Lyu – ACS Infectious Diseases

Human and General Microbiome

Multilocus-sequence typing reveals clonality of Staphylococcus aureus in atopic dermatitis – Leszek Blicharz – Clinical and Experimental Dermatology

Metabarcoding approach to identify bacterial community profiling related to nosocomial infection and bacterial trafficking-routes in hospital environments – Bárbara Gimenes de Castro – Journal of Toxicology and Environmental Health. Part A

Identification of host gene-microbiome associations in colorectal cancer patients using mendelian randomization – Yaoxian Xiang – Journal of Translational Medicine

Bacterial amylases enable glycogen degradation by the vaginal microbiome – Dominick J Jenkins – Nature Microbiology

Babies, bugs and brains: How the early microbiome associates with infant brain and behavior development – Sebastian Hunter – PloS One

A retrospective analysis of vitamin B6 deficiency and associated changes of gut microbes in Crohn’s disease – Zhongsheng Feng – European Journal of Clinical Nutrition

The intestinal microbiota predicts COVID-19 severity and fatality regardless of hospital feeding method – Vanni Bucci – mSystems

Commentary and Views: The importance of the gut microbiome in the pathogenesis and transmission of SARS-CoV-2 – Carlo Brogna – Gut Microbes

Meta-analysis: Perturbations in gut microbiota composition in patients with polycystic ovary syndrome: a systematic review and meta-analysis – Pan Li – BMC Medicine

Letter: Caution regarding the specificities of pan-cancer microbial structure – Abraham Gihawi – Microbial Genomics

Review: Gut microbial beta-glucuronidase: a vital regulator in female estrogen metabolism – Shiwan Hu – Gut Microbes

Review: Three specific gut bacteria in the occurrence and development of colorectal cancer: a concerted effort – Dengmei Gong – PeerJ

Animal Microbiome (models and non-model organisms)

Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China – Michelle Baker – Nature Food

The enhancement in toxic potency of oxidized functionalized polyethylene-microplastics in mice gut and Caco-2 cells – Ji Wang – The Science of the Total Environment

Review: Geroprotective potential of microbiome modulators in the Caenorhabditis elegans model – Brandi C Miller – GeroScience

Microbiome Ecology and Evolution

Macroevolutionary constraints on global microbial diversity – Ford J Fishman – Ecology and Evolution

Evolutionary dynamics on sequential temporal networks – Anzhi Sheng – PLoS Computational Biology

Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community – Anna S Weiss – Nature Communications

Extremophiles

Earth to Mars: A Protocol for Characterizing Permafrost in the Context of Climate Change as an Analog for Extraplanetary Exploration – Kimberley R Miner – Astrobiology

Bioleaching of polymetallic sulphidic mining residues: influence of increasing solid concentration on microbial community dynamics and metal dissolution – Catherine Joulian – Research in Microbiology

Environmental Microbiome

Multidimensional specialization and generalization are pervasive in soil prokaryotes – Damian J Hernandez – Nature Ecology & Evolution

Metagenome Analysis of Speleothem Microbiome from Subterranean Cave Reveals Insight into Community Structure, Metabolic Potential, and BGCs Diversity – Brajogopal Samanta – Current Microbiology

Effects of marine sediment as agricultural substrate on soil microbial diversity: an amplicon sequencing study – Dámaris Núñez-Gómez – Environmental Microbiome

Opinion: New microbial tools to boost restoration and soil organic matters – Tadeo Sáez-Sandino – Microbial Biotechnology

Microbiome Research: Resources, Tools and Techniques

Optimization of fecal sample homogenization for untargeted metabolomics – Kieran Tarazona Carrillo – Metabolomics : Official Journal of the Metabolomic Society

metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering – Chunlin Hao – Microbiome

sccomp: Robust differential composition and variability analysis for single-cell data – Stefano Mangiola – PNAS

Metagenome sequencing and 103 microbial genomes from ballast water and sediments – Zhaozhao Xue – Scientific Data