Monthly Archives: September 2023

September 27, 2023

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General microbiome

The Triple Alliance: Microbiome, Mitochondria, and Metabolites in the Context of Age-Related Cognitive Decline and Alzheimer’s Disease – Prajapiti et al. – The Journals of Gerontology: Series A

[REVIEW]Genomic surveillance for antimicrobial resistance — a One Health perspective – Djordjevic et al. – Nature Reviews Genetics

Human respiratory microbiome

[REVIEW]Lung Microbiome as a Treatable Trait in Chronic Respiratory Disorders – Scialo et al. – Lung

Human gut microbiome

[PREPRINT]Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation – Xue et al. – bioRxiv

[PREPRINT]A gut meta-interactome map reveals modulation of human immunity by microbiome effectors – Young et al. – bioRxiv

[PREPRINT]Association of homelessness and diet on the gut microbiome: A United States-Veteran Microbiome Project (US-VMP) study – Hoisington et al. – bioRxiv

Plant, root, and soil microbiome

Tomato growth stage modulates bacterial communities across different soil aggregate sizes and disease levels – Dong et al. – ISME Communications

Soil microbial diversity and network complexity drive the ecosystem multifunctionality of temperate grasslands under changing precipitation – Zhai et al. – Science of The Total Environment

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

Arctic bacterial diversity and connectivity in the coastal margin of the Last Ice Area – Girard, Vincent & Culley – ISME Communications

A glimpse of the paleome in endolithic microbial communities – Wegener et al. – Microbiome

Bioinformatics

A computational method to dissect colonization resistance of the gut microbiota against pathogens – Ke et al. – Cell Reports Methods

[PREPIRNT]SurvBal: Compositional Microbiome Balances for Survival Outcomes – Li et al. – bioRxiv

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