December 23, 2023

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Happy Holidays, from the MicrobiomeDigest team!

Human and General Microbiome

Gut microbiota predicts severity and reveals novel metabolic signatures in acute pancreatitis – Christoph Ammer-Herrmenau – Gut

Human gut microbiota from hepatitis B virus-infected individuals is associated with reduced triglyceride level in mice: faecal transplantation study – Han-Na Kim – Microbes and Infection

Commensal bacteria maintain a Qa-1(b)-restricted unconventional CD8(+) T population in gut epithelium – Jian Guan – eLife

Akkermansia muciniphila – friend or foe in colorectal cancer? – Ekaterina O Gubernatorova – Frontiers in Immunology

Association between erythrocyte membrane fatty acids and gut bacteria in obesity-related cognitive dysfunction – Tong Zhao – AMB Express

Impact of the gut microbiome on immunological responses to COVID-19 vaccination in healthy controls and people living with HIV – Shilpa Ray – NPJ Biofilms and Microbiomes

The relationship between sleep, gut microbiota, and metabolome in patients with depression and anxiety: A secondary analysis of the observational study – Arisa Tanaka – PloS ONE

Persistence of gut dysbiosis in individuals with anorexia nervosa – Yukiko Morisaki – PloS ONE

Unique microbial diversity, community composition, and networks among Pacific Islander endocervical and vaginal microbiomes with and without Chlamydia trachomatis infection in Fiji – Sankhya Bommana – mBio

Gut microbiome-based machine learning for diagnostic prediction of liver fibrosis and cirrhosis: a systematic review and meta-analysis – Xiaopei Liu – BMC Medical Informatics and Decision Making

Targeting gut microbial nitrogen recycling and cellular uptake of ammonium to improve bortezomib resistance in multiple myeloma – Yinghong Zhu – Cell Metabolism

Variations in the oral microbiome and metabolome of methamphetamine users – Dawei Wang – mSystems

Investigating the causal impact of gut microbiota on glioblastoma: a bidirectional Mendelian randomization study – Chuan Zeng – BMC Genomics

Alterations of oral and gut viromes in hypertension and/or periodontitis – Hui-Lin Ye – mSystems

Heterogeneous associations of gut microbiota with Crohn’s disease activity – Susanne Pinto – Gut Microbes

Early / Infant / Children Microbiome

Gut-resident microorganisms and their genes are associated with cognition and neuroanatomy in children – Kevin S Bonham – Science Advances

The association of tonsillar microbiota with biochemical indices based on obesity and tonsillar hypertrophy in children – Jiwon Park – Scientific Reports

Synergistic horizontal transfer of antibiotic resistance genes and transposons in the infant gut microbial genome – Yanwen Ding – mSphere

Beneficial Microbes and Compounds

Potential therapeutic implications of histidine catabolism by the gut microbiota in NAFLD patients with morbid obesity – Sergio Quesada-Vázquez – Cell Reports Medicine

Attenuation of allergen-specific immunotherapy for atopic dermatitis by ectopic colonization of Brevundimonas vesicularis in the intestine – Xiaochun Liu – Cell Reports Medicine

Model and Non-Model Animal Microbiome

The influence of diet on gut microbiome and body mass dynamics in a capital-breeding migratory bird – Isabelle Jones – PeerJ

Autophagic dysfunction and gut microbiota dysbiosis cause chronic immune activation in a Drosophila model of Gaucher disease – Magda L Atilano – PLoS Genetics

Cytolethal distending toxin B inoculation leads to distinct gut microtypes and IBS-D-like microRNA-mediated gene expression changes in a rodent model – Gabriela Leite – Gut Microbes

Microbiome and Evolution

Evolutionary patterns and processes in animal microbiomes – Florent Mazel – Journal of Evolutionary Biology

Plant and Soil Microbiome

Wheat fungal endophyte communities are inseparable from the host and influence plant development – Or Sharon – mBio

Environmental Microbiome

Metagenomics-Based Microbial Ecological Community Threshold and Indicators of Anthropogenic Disturbances in Estuarine Sediments – Yingyu Bao – Environmental Science & Technology

Microbiome Analysis: Tools, Techniques and Resources

Review: Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology – Corinne Walsh – mBio

SOHPIE: Statistical Approach via Pseudo-Value Information and Estimation for Differential Network Analysis of Microbiome Data – Seungjun Ahn – Bioinformatics

Examining the functional space of gut microbiome-derived peptides – Ying-Chiang J Lee – MicrobiologyOpen

A new absolute quantitative method for peptide and metabolite detection – Carlo Brogna – Journal of Mass Spectrometry

Next steps in studying host-microbiome interactions in apical periodontitis – Athina C Georgiou – Frontiers in Oral Health

December 18, 2023

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Human and General Microbiome

Microbiome diversity protects against pathogens by nutrient blocking – Frances Spragge – Science 

Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients – Zixuan Xie – Microbiome

Functional alterations and predictive capacity of gut microbiome in type 2 diabetes – Nihar Ranjan Dash – Scientific Reports

Fecal metabolite profiling identifies liver transplant recipients at risk for postoperative infection – Christopher J Lehmann – Cell Host & Microbe

Establishment of oral microbiome in very low birth weight infants during the first weeks of life and the impact of oral diet implementation – Pedro A R Vanzele – PloS One

Infant gut DNA bacteriophage strain persistence during the first 3 years of life – Yue Clare Lou – Cell Host & Microbe

Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition – Elias R Gerrick – Cell

Poly-omic risk scores predict inflammatory bowel disease diagnosis – Christopher H Arehart – mSystems

Review: Impact of glyphosate (Roundup(TM)) on the composition and functionality of the gut microbiome – Lauren Walsh – Gut Microbes

Rapid turnover and short-term blooms of Escherichia coli in the human gut – Na Han – Journal of Bacteriology

Designing a multi-epitope vaccine against Peptostreptococcus anaerobius based on an immunoinformatics approach – Yudan Mao – Synthetic and Systems Biotechnology

Twnbiome: a public database of the healthy Taiwanese gut microbiome – Amrita Chattopadhyay – BMC Bioinformatics

Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting – Alessandra Riva – Nature Communications

Review: Application of omics technologies in cariology research: A critical review with bibliometric analysis – Josie Shizhen Zhang – Journal of Dentistry

Dysbiosis and associated stool features improve prediction of response to biological therapy in inflammatory bowel disease – Clara Caenepeel – Gastroenterology

Highlight: Female Reproductive Tract Microbiome

Review: Culturomics in Unraveling the Upper Female Reproductive Tract Microbiota – Robin Vanstokstraeten – Seminars in Reproductive Medicine

A manifold-based framework for studying the dynamics of the vaginal microbiome – Mor Tsamir-Rimon – NPJ Biofilms and Microbiomes

Culturomics reveals a hidden world of vaginal microbiota with the isolation of 206 bacteria from a single vaginal sample – Linda Abou Chacra – Archives of Microbiology

Effects of variation in sample storage conditions and swab order on 16S vaginal microbiome analyses – Tanya Kumar – Microbiology Spectrum

Non-Model Animal Microbiome

Activity budget and gut microbiota stability and flexibility across reproductive states in wild capuchin monkeys in a seasonal tropical dry forest – Shasta E Webb – Animal Microbiome

Validation of method for faecal sampling in cats and dogs for faecal microbiome analysis – Xavier Langon – BMC Veterinary Research

Transmission of antimicrobial resistance in the gut microbiome of gregarious cockroaches: the importance of interaction between antibiotic exposed and non-exposed populations – Amalia Bogri – mSystems

Plant and Soil Microbiome

Fungal community composition changes and reduced bacterial diversity drive improvements in the soil quality index during arable land restoration – Pingxing Wan – Environmental Research

Two-for-one: root microbiota orchestrates both soil pH and plant nutrition – João Antonio Siqueira – Trends in Plant Science

Cotton microbiome profiling and Cotton Leaf Curl Disease (CLCuD) suppression through microbial consortia associated with Gossypium arboreum – Rhea Aqueel – NPJ Biofilms and Microbiomes

Environmental Microbiome

Benthic microbial biogeographic trends in the North Sea are shaped by an interplay of environmental drivers and bottom trawling effort – Guido Bonthond – ISME Communications

Increased prokaryotic diversity in the Red Sea deep scattering layer – Tamara Megan Huete-Stauffer – Environmental Microbiome

December 15, 2023

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Today’s digest features house mice gut microbiome, infant gut DNA bacteriophage strain persistence, maternal gut microbiome in pregnancy, and more.

Do not miss Francine Marques’s opinion on rethinking culture to unlock the potential of research.

See you at #MVIF next week!

Respiratory microbiome

Review: Winds of change a tale of: asthma and microbiome – David Galeana-Cadena – Frontiers in Microbiology

Gut microbiome

Review: The maternal gut microbiome in pregnancy: implications for the developing immune system – Omry Koren – Nature Reviews Gastroenterology & Hepatology

Bioactive glycans in a microbiome-directed food for children with malnutrition – Matthew C. Hibberd – Nature

Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients – Zixuan Xie – Microbiome

Gut microbiota-related metabolite alpha-linolenic acid mitigates intestinal inflammation induced by oral infection with Toxoplasma gondii – Jing Yang – Microbiome

Fiber-deficient diet inhibits colitis through the regulation of the niche and metabolism of a gut pathobiont – Peter Kuffa – Cell Host & Microbe

Animal microbiome

Subspecies divergence, hybridisation and the spatial environment shape phylosymbiosis in the microbiome of house mice – Susana C. M. Ferreira – bioRxiv

Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers – Gilles L. C. Baud – Genome Biology

Seasonal and environmental factors contribute to the variation in the gut microbiome: a large-scale study of a small bird – Martta Liukkonen – bioRxiv

Plant-Root-Soil microbiome

Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota – Nathan Vannier – Nature Communications

Virome

Infant gut DNA bacteriophage strain persistence during the first 3 years of life – Yue Clare Lou – Cell Host & Microbe

Techniques

High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities – Patrick Müller – Nature Protocols

Bioinformatics

MAGqual: A standalone pipeline to assess the quality of metagenome-assembled genomes – James P.J. Chong – bioRxiv

December 10, 2023

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General and Human Microbiome

Altered gut microbiome associated with metabolic-associated fatty liver disease in Chinese children – Jing Ji – Clinical Nutrition (Edinburgh, Scotland)

Airway environment drives the selection of quorum sensing mutants and promote Staphylococcus aureus chronic lifestyle – Xiongqi Ding – Nature Communications

Review: Gut microbiota in overweight and obesity: crosstalk with adipose tissue – Patrice D Cani – Nature Reviews. Gastroenterology & Hepatology

Review: Recent advances in single-cell engineered live biotherapeutic products research for skin repair and disease treatment – Muhamad Aidilfitri Mohamad Roslan – NPJ Biofilms and Microbiomes

Metaproteomic assessment of gut microbial and host functional perturbations in Helicobacter pylori-infected patients subjected to an antimicrobial protocol – Marcello Abbondio – Gut Microbes

The facial microbiome and metabolome across different geographic regions – Rong Tao – Microbiology Spectrum

Periodontitis salivary microbiota exacerbates colitis-induced anxiety-like behavior via gut microbiota – Jun Qian – NPJ Biofilms and Microbiomes

Vasoactive intestinal polypeptide plays a key role in the microbial-neuroimmune control of intestinal motility – Xiaopeng Bai – Cellular and Molecular Gastroenterology and Hepatology

Multi-omics analyses reveal bacteria and catalase associated with keloid disease – Mengjie Shan – EBioMedicine

Beneficial Microbes and Compounds

Genomic and Phenotypic Insight into the Probiotic Potential of Lactic Acid Bacterial spp. Associated with the Human Gut Mucosa – Kanwal Aziz – Probiotics and Antimicrobial Proteins

Review: A review on the use of prebiotics in ulcerative colitis – James M Kennedy – Trends in Microbiology

Oral magnesium prevents acetaminophen-induced acute liver injury by modulating microbial metabolism – Dongping Li – Cell Host & Microbe

Review: Akkermansia muciniphila and Alcohol-Related Liver Diseases. A Systematic Review – Lydie Sparfel – Molecular Nutrition & Food Research

Review: Triangulating nutrigenomics, metabolomics and microbiomics toward personalized nutrition and healthy living – George Lagoumintzis – Human Genomics

Non-Model Animal Microbiome 

The role of diet and host species in shaping the seasonal dynamics of the gut microbiome – Claire E Williams – FEMS Microbiology Ecology

Increased environmental microbial diversity reduces the disease risk of a mosquitocidal pathogen – Zhiwei Kang – mBio

Plant and Soil Microbiome

Characterization of microbial contamination in agricultural soil: A public health perspective – Xiaodi Li – The Science of the Total Environment

Metagenomics reveals effects of fluctuating water conditions on functional pathways in plant litter microbial community – Matevž Likar – Scientific Reports

Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease – Yanyan Zhou – Nature Communications

Environmental Microbiome

Environmental determinants and demographic influences on global urban microbiomes, antimicrobial resistance and pathogenicity – Yang Chen – NPJ Biofilms and Microbiomes

Multiple spatial scales of bacterial and fungal structural and functional traits affect carbon mineralization – Zhiyuan Ma – Molecular Ecology

Microbiome Analysis: tools, techniques and resources

Review: Establishing genetic manipulation for novel strains of human gut bacteria – Paul O Sheridan – Microbiome Research Reports

December 6, 2023

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Human salivary microbiome

Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer – de Medeiros et al. – Microbiome

Human skin microbiome

[PREPRINT]Commensal skin bacteria exacerbate inflammation and delay skin healing – Khadka et al. – bioRxiv

Human vaginal microbiome

Integrating compositional and functional content to describe vaginal microbiomes in health and disease – Holm et al. – Microbiome

Comparison of vaginal microbiota between women with inflammatory bowel disease and healthy controls – Bar et al. – PLOS One

Human gut microbiome

Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis—a case study using metatranscriptomics – Deng et al. – Microbiome

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Vitamin D modulation of brain-gut-virome disorder caused by polystyrene nanoplastics exposure in zebrafish (Danio rerio) – Teng et al – Microbiome

Animal microbiome (for animals in the wild)

Diversity of gut microbiome in Rocky Mountainsnail across its native range – Chalifour, Elder & Li – PLOS One

[PREPRINT]Testing the effectiveness of a commercially sold probiotic on restoring the gut microbiota of honey bees: a field study – Damico et al. – bioRxiv

Core gut microbes Cloacibacterium and Aeromonas associated with different gastropod species could be persistently transmitted across multiple generations – Lin et al. – Microbiome

Plant, root, and soil microbiome

Effects of multiple N, P, and K fertilizer combinations on strawberry growth and the microbial community – Bai et al. – PLOS One

Comparison of microbial community assemblages in the rhizosphere of three Amaranthus spp. – Chee-Sanford & Connor – PLOS One

Bioinformatics

Phantom oscillations in principal component analysis – Shinn – PNAS
This phenomenon is not new (e.g. know as horseshoe effect) but Shinn gives a very understandable explanation.

The MAGMA pipeline for comprehensive genomic analyses of clinical Mycobacterium tuberculosis samples – Heupink et al. – PLOS Computational Biology

[PREPRINT]metaExpertPro: a computational workflow for metaproteomics spectral library construction and data-independent acquisition mass spectrometry data analysis – Sun et al. – bioRxiv

[PREPRINT]MolPad: An R-Shiny Package for Cluster Co-Expression Analysis in Longitudinal Microbiomics – Ma, Thairu & Sankaran

November 28, 2023

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Pregnancy and early life

[PREPRINT]Delivery mode impacts gut bacteriophage colonization during infancy – Subramanian et al. – medRxiv

Human oral microbiome

Oral microbiota analyses of paediatric Saudi population reveals signatures of dental caries – Alyousef et al. – BMC Oral Health

Human gut microbiome

Gastric coinfection with thiopeptide-positive Cutibacterium acnes decreases FOXM1 and pro-inflammatory biomarker expression in a murine model of Helicobacter pylori-induced gastric cancer – Lunger et al. – Microbiology Spectrum

[REVIEW]Butterflies in the gut: the interplay between intestinal microbiota and stress – Lai et al. – Journal of Biomedical Science

[REVIEW]Genetics, Nutrition, and Health: A New Frontier in Disease Prevention – Agrawal et al. – Journal of the American Nutrition Association

Age-dependent changes in the gut microbiota and serum metabolome correlate with renal function and human aging – Sun et al. – Aging Cell

The changes of gut microbiota and metabolites in different drug-induced liver injuries – Zhu et al. – Journal of Medical Microbiology

[PREPRINT]The differing prevalences of propionate and butyrate producing bacteria in the human gut microbiota – Christensen et al. – bioRxiv

[PREPRINT]The Parkinson’s drug entacapone disrupts gut microbiome homeostasis via iron sequestration – Pereira et al. – bioRxiv

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Mutual modulation of gut microbiota and the immune system in type 1 diabetes models – Rosell-Mases et al. – Nature Communications

[PREPRINT]Microbiota-dependent early life programming of gastrointestinal motility – Frith et al. – bioRxiv

Horizontal transmission of gut microbiota attenuates mortality in lung fibrosis – Gurczynski et al. – JCI insight

High-altitude and low-altitude adapted chicken gut-microbes have different functional diversity – Bhagat et al. – Scientific Reports

Animal microbiome (for animals in the wild)

Introducing an environmental microbiome to axenic Aedes aegypti mosquitoes documents bacterial responses to a blood meal – LaReau et al. – Applied and Environmental Microbiology

Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer – Zhuang et al. – Microbiology Spectrum

Plant, root, and soil microbiome

[PREPRINT]Global patterns in gene content of soil microbiomes emerge from microbial interactions – Crocker et al. – bioRxiv

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

Metagenomic analysis reveals diverse microbial community and potential functional roles in Baner rivulet, India – Brar et al. – Journal of Genetic Engineering and Biotechnology

Bioinformatics

mb-PHENIX: Diffusion and Supervised Uniform Manifold Approximation for denoising microbiota data – Padron-Manrique et al. – Bioinformatics

Facilitating bioinformatics reproducibility with QIIME 2 provenance Replay – Keefe et al. – PLOS Computational Biology

Techniques

High-throughput identification and quantification of bacterial cells in the microbiota based on 16S rRNA sequencing with single-base accuracy using BarBIQ – Jin, Yamamoto & Shiroguchi

November 27, 2023

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Human and General Microbiome

Multi-site microbiota alteration is a hallmark of kidney stone formation – Kait F Al – Microbiome

Culturing the unculturables: strategies, challenges, and opportunities for gut microbiome study – Asha Yadav – Journal of Applied Microbiology

Trans-vaccenic acid reprograms CD8(+) T cells and anti-tumour immunity – Hao Fan – Nature

Multi-omics analysis of hospital-acquired diarrhoeal patients reveals biomarkers of enterococcal proliferation and Clostridioides difficile infection – Marijana Bosnjak – Nature Communications

Why are so many enteric pathogen infections asymptomatic? Pathogen and gut microbiome characteristics associated with diarrhea symptoms and carriage of diarrheagenic E. coli in northern Ecuador – Kelsey J Jesser – Gut Microbes

Gut microbiome and frailty: insight from genetic correlation and mendelian randomization – Guanghui Cui – Gut Microbes

Review: Metabolic exchanges are ubiquitous in natural microbial communities – Christian Kost – Nature Microbiology

Review: Evolution of a Pathogenic Microbiome – Pui Yin Wong – Journal of Clinical Medicine

Review: Evidence for the contribution of the gut microbiome to obesity and its reversal – Douwe F de Wit – Science Translational Medicine

Beneficial Microbes and Compounds

Parabacteroides distasonis ameliorates insulin resistance via activation of intestinal GPR109a – Yonggan Sun – Nature Communications

Galactooligosaccharide Mediates NF-κB Pathway to Improve Intestinal Barrier Function and Intestinal Microbiota – Menglu Xi – Molecules 

A self-stabilized and water-responsive deliverable coenzyme-based polymer binary elastomer adhesive patch for treating oral ulcer – Chunyan Cui – Nature Communications

A key genetic factor governing arabinan utilization in the gut microbiome alleviates constipation – Chengcheng Zhang – Cell Host & Microbe

Meta-analysis: Fiber intake and fiber intervention in depression and anxiety: a systematic review and meta-analysis of observational studies and randomized controlled trials – Hajara Aslam – Nutrition Reviews

Animal Microbiome

Identification of peptides from honeybee gut symbionts as potential antimicrobial agents against Melissococcus plutonius – Haoyu Lang – Nature Communications

A coral-associated actinobacterium mitigates coral bleaching under heat stress – Jie Li – Environmental Microbiome

Symbiodiniaceae photophysiology and stress resilience is enhanced by microbial associations – Jennifer L Matthews – Scientific Reports

Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts – Dan Sun – ISME Communications

Experimental mining plumes and ocean warming trigger stress in a deep pelagic jellyfish – Vanessa I Stenvers – Nature Communications

Gut microbiomes of cycad-feeding insects tolerant to β-methylamino-L-alanine (BMAA) are rich in siderophore biosynthesis – Karina Gutiérrez-García – ISME Communications

Environmental Factors and the Symbiont Cardinium Influence the Bacterial Microbiome of Spider Mites Across the Landscape – Huan-Huan Liu – Microbial Ecology

Animal Model Microbiome

Gut microbiota-bile acid crosstalk regulates murine lipid metabolism via the intestinal FXR-FGF19 axis in diet-induced humanized dyslipidemia – Hongtao Xu – Microbiome

Multi-omics data reveals aberrant gut microbiota-host glycerophospholipid metabolism in association with neuroinflammation in APP/PS1 mice – Xiaohang Qian – Gut Microbes

Plant and Environmental Microbiome

Combined application of microbial inoculant and kelp-soaking wastewater promotes wheat seedlings growth and improves structural diversity of rhizosphere microbial community – Xin Song – Scientific Reports

Contribution of ammonia-oxidizing archaea and bacteria to nitrogen transformation in a soil fertilized with urea and organic amendments – Yajun Yang – Scientific Reports

Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost – Karl J Romanowicz – ISME Communications

Microbiome Analysis: tools, techniques, and resources

PanDelos-frags: A methodology for discovering pangenomic content of incomplete microbial assemblies – Vincenzo Bonnici – Journal of Biomedical Informatics

PLM-ARG: antibiotic resistance gene identification using a pretrained protein language model – Jun Wu – Bioinformatics

Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes – Shreya Arya – PNAS

Vaccinomics-aided next-generation novel multi-epitope-based vaccine engineering against multidrug resistant Shigella sonnei: Immunoinformatics and chemoinformatics approaches – Sara Aiman – PloS One

Detecting host responses to microbial stimulation using primary epithelial organoids – Jette Bornholdt – Gut Microbes

Review: Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities – Suleiman Aminu – Critical Reviews in Microbiology

November 20, 2023

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Human and General Microbiome

Association between microbiome and the development of adverse posttraumatic neuropsychiatric sequelae after traumatic stress exposure – Abigail L Zeamer – Translational Psychiatry

The preterm human milk microbiota fluctuates by postpartum week and is characterized by gestational age and maternal BMI – Evgenia Jen Filatava – mBio

Strain-resolved metagenomic analysis of the gut as a reservoir for bloodstream infection pathogens among premature infants in Singapore – Sarah M Heston – Gut Pathogens

Porphyromonas gingivalis as a promotor in the development of the alcoholic liver disease via ferroptosis – Chao Yao – Microbes and Infection

The core phageome and its interrelationship with preterm human milk lipids – Wen C Yew – Cell Reports

Longitudinal analysis at three oral sites links oral microbiota to clinical outcomes in allogeneic hematopoietic stem-cell transplant – Vitor Heidrich – Microbiology Spectrum

Gut inflammation associated with age and Alzheimer’s disease pathology: a human cohort study – Margo B Heston – Scientific Reports

Robust airway microbiome signatures in acute respiratory failure and hospital-acquired pneumonia – Emmanuel Montassier – Nature Medicine

Beneficial Microbes and Compounds

Systematic mining of the human microbiome identifies antimicrobial peptides with diverse activity spectra – Andrew M King – Nature Microbiology

Skin benefits of postbiotics derived from Micrococcus luteus derived from human skin: an untapped potential for dermatological health – Young Mok Heo – Genes & Genomics

Akkermansia muciniphila attenuated lipopolysaccharide-induced acute lung injury by modulating the gut microbiota and SCFAs in mice – Jian Shen – Food & Function

Review: The Potential of Meta-Proteomics and Artificial Intelligence to Establish the Next Generation of Probiotics for Personalized Healthcare – Arpita Das – Journal of Agricultural and Food Chemistry

Review: Gut microbiome in healthy aging versus those associated with frailty – Mi Young Lim – Gut Microbes

Animal Microbiome

Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome – Javad Sadeghi – Microbiome

Aedes aegypti microbiome composition covaries with the density of Wolbachia infection – Jane Pascar – Microbiome

Sequential host-bacteria and bacteria-bacteria interactions determine the microbiome establishment of Nematostella vectensis – H Domin – Microbiome

Microbial symbionts are shared between ants and their associated beetles – Catalina Valdivia – Environmental Microbiology

The gut microbiome mediates adaptation to scarce food in Coleoptera – Oana Teodora Moldovan – Environmental Microbiome

Animal Model Microbiome

Interplay of gut microbiota and host epithelial mitochondrial dysfunction is necessary for the development of spontaneous intestinal inflammation in mice – Kibrom M Alula – Microbiome

Environmental Microbiome

Microbial diversity and community structure dynamics in acid mine drainage: Acidic fire with dissolved heavy metals – Wasim Sajjad – The Science of the Total Environment

Polar lake microbiomes have distinct evolutionary histories – Bjorn Tytgat – Science Advances

Plant Microbiome

PSKR1 balances the plant growth-defence trade-off in the rhizosphere microbiome – Siyu Song – Nature Plants

Streptomyces alleviate abiotic stress in plant by producing pteridic acids – Zhijie Yang – Nature Communications

Microbiome Analysis: tools, techniques and resources

The pan-microbiome profiling system Taxa4Meta identifies clinical dysbiotic features and classifies diarrheal disease – Qinglong Wu – The Journal of Clinical Investigation

Review: Machine learning for microbiologists – Francesco Asnicar – Nature Reviews. Microbiology

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November 10, 2023

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Read about new species discovered in the female genitourinary tract Lactobacillus isalae, Gardnerella pickettii and Gardnerella greenwoodii, and important UTI and other latest microbiome science news.
Happy Friday! And see you next week at MVIF!

Urinary microbiome

A human urothelial microtissue model reveals shared colonization and survival strategies between uropathogens and commensals – Carlos Flores – Science Advances

Gardnerella pickettii sp. nov. (formerly Gardnerella genomic species 3) and Gardnerella greenwoodii sp. nov. (formerly Gardnerella genomic species 8) isolated from female urinary microbiome – Márcia Sousa – International Journal of Systematic and Evolutionary Microbiology

Vaginal microbiome

Lactobacillus isalae sp. nov., isolated from the female reproductive tract – Tom Eilers – International Journal of Systematic and Evolutionary Microbiology

Identification of a DNA-cytosine methyltransferase that impacts global transcription to promote group B streptococcal vaginal colonization – Haider S. Manzer – mBio

Gut microbiome

Aggression: A gut reaction? The effects of the gut microbiome on aggression – Atara Uzan-Yulzari – bioRxiv

Oral microbiome

Establishment of tongue microbiota by 18 months of age and determinants of its microbial profile – Shinya Kageyama – mBio

Animal microbiome

Pet cats may shape the antibiotic resistome of their owner’s gut and living environment – Yiwen Yang – Microbiome

The impact of kit, environment and sampling contamination on the observed microbiome of bovine milk – Christopher J Dean – bioRxiv

Animal experiments

Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease – Lola Holcomb – mSystems

Daily fluctuation of colonic microbiome in response to nutrient substrates in a pig model – Hongyu Wang – npj Biofilms and Microbiomes

Water microbiome

Assessing the impact of anti-microbial showerheads on the prevalence and abundance of opportunistic pathogens in shower water and shower water-associated aerosols – Sarah Pitell, Sarah-Jane Haig – Frontiers in Microbiomes

Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants – Huifeng Hu – bioRxiv

Technique

A high-throughput and low-waste viability assay for microbes – Christian T. Meyer – Nature Microbiology

Bioinformatics

Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses – Saioa Manzano-Morales – Genome Biology

ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool – Hoon Je Seong – Briefings in Bioinformatics


November 6, 2023

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Human Gut Microbiome

Altered Gut Microbiota and Short-chain Fatty Acids in Chinese Children with Constipated Autism Spectrum Disorder – Jianquan He – Scientific Reports

Clostridium butyricum and Clostridium tyrobutyricum: angel or devil for necrotizing enterocolitis? – Ruizhi Tao – mSystems

Gut microbiota composition and diversity before, during, and two months after rifamycin-based tuberculosis preventive therapy – Marie Nancy Séraphin – Scientific Reports

Genomic analyses of Bacteroides fragilis: subdivisions I and II represent distinct species – Jamie English – Journal of Medical Microbiology

Bacterial SNPs in the human gut microbiome associate with host BMI – Liron Zahavi – Nature Medicine

Fecal short-chain fatty acids in non-constipated irritable bowel syndrome: a potential clinically relevant stratification factor based on catabotyping analysis – Giorgio Gargari – Gut Microbes

Characterizing alterations in the gut microbiota following postpartum weight change – Bridget N Chalifour – mSystems

Core-genome multilocus sequence typing and core-SNP analysis of Clostridium neonatale strains isolated in different spatio-temporal settings – Victoria Mesa – Microbiology Spectrum

Human Microbiome (outside the gut)

Identification of root canal microbiota profiles of periapical tissue diseases using matrix-assisted laser desorption/ionization time-of-flight mass spectrometer – Mete Ahlat – Anaerobe

Gardnerella pickettii sp. nov. (formerly Gardnerella genomic species 3) and Gardnerella greenwoodii sp. nov. (formerly Gardnerella genomic species 8) isolated from female urinary microbiome – Márcia Sousa – International Journal of Systematic and Evolutionary Microbiology

Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population – Giacomo Antonello – Scientific Reports

Prolonged mask wearing changed nasal microbial characterization of young adults during the COVID-19 pandemic in Shanghai, China – Guoxiu Xiang – Frontiers in Immunology

Beneficial Microbes, Compounds and Interventions

Inulin-enriched Megamonas funiformis ameliorates metabolic dysfunction-associated fatty liver disease by producing propionic acid – Xinyue Yang – NPJ Biofilms and Microbiomes

A gut microbial metabolite of linoleic acid ameliorates liver fibrosis by inhibiting TGF-β signaling in hepatic stellate cells – Nanaho Kasahara – Scientific Reports

Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement – Michael H Woodworth – Science Translational Medicine

Animal Microbiome

Revealing the developmental characterization of rumen microbiome and its host in newly received cattle during receiving period contributes to formulating precise nutritional strategies – Yanjiao Li – Microbiome

Shifts in the coral microbiome in response to in situ experimental deoxygenation – Rachel D Howard – Applied and Environmental Microbiology

Limitation of amino acid availability by bacterial populations during enhanced colitis in IBD mouse model – Tanner G Richie – mSystems

Estradiol mediates colonic epithelial protection in aged mice after stroke and is associated with shifts in the gut microbiome – Juneyoung Lee – Gut Microbes

Functional potential and evolutionary response to long-term heat selection of bacterial associates of coral photosymbionts – Justin Maire – mSystems

Gut bacteria mediated adaptation of diamondback moth, Plutella xylostella, to secondary metabolites of host plants – Xiaofeng Xia – mSystems

Environmental Microbiome

Microbial hitchhikers harbouring antimicrobial-resistance genes in the riverine plastisphere – Vinko Zadjelovic – Microbiome

Taxonomic distribution of metabolic functions in bacteria associated with Trichodesmium consortia – Coco Koedooder – mSystems

Review: Microbial ecology of drinking water from source to tap – Leili Abkar – The Science of the Total Environment

Microbiome Analysis: Tools, Techniques and Resources

Food4healthKG: Knowledge graphs for food recommendations based on gut microbiota and mental health – Chengcheng Fu – Artificial Intelligence in Medicine

Testing latent classes in gut microbiome data using generalized Poisson regression models – Xinhui Qiao – Statistics in Medicine