Category Archives: Plant Root Soil microbiome

May 29, 2024

Posted on by

Human microbiomes

Gut microbiome remodeling and metabolomic profile improves in response to protein pacing with intermittent fasting versus continuous caloric restriction – Alex E. Mohr – Nature Communications

[PREPRINT] Towards a Health-Associated Core Keystone (HACK) index for the human gut microbiome – Abishek Goel – bioRxiv

Exposure to environmental pollutants selects for xenobiotic-degrading functions in the human gut microbiome – Francesca De Fillipis – Nature Communications

The interrelation between microbial immunoglobulin coating, vaginal microbiota, ethnicity, and preterm birth – H.J. Schuster – BMC Microbiome

Porphyromonas gingivalis, a bridge between oral health and immune evasion in gastric cancer – Matías Muñoz-Medel – Frontiers in Oncology

Differences in maternal subgingival microbiome between preterm and term births: The MOHEPI study – Jung Soo Park – Journal of Periodontal Resaerch

Animal microbiome

Integrating uterine microbiome and metabolome to advance the understanding of the uterine environment in dairy cows with metritis – S. Casaro – BMC Animal Microbiome

Responses of nutrient utilization, rumen fermentation and microorganisms to different roughage of dairy buffaloes – Shichun He – BMC Microbiology

Identification of the mutual gliding locus as a factor for gut colonization in non-native bee hosts using the ARTP mutagenesis – Yujie Meng – BMC Microbiome

Co-habiting ants and silverfish display a converging feeding ecology – Thomas Parmentier – BMC Biology

Temperature-dependent differences in mouse gut motility are mediated by stress – Alvin Han – Nature Lab Animal

Food microbiome

Evaluation of microbiota-induced changes in biochemical, sensory properties and volatile profile of kombucha produced by reformed microbial community – Hilal Kilmanoglu – Food Chemistry X

Plant, soil, and root microbiome

Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle – Bridget B. McGivern – Nature Microbiology

[PREPRINT] Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils – Samuel E. Barnett & Ashley Shade – bioRxiv

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome – Yoko Masuda – BMC Microbiome

Water & extremophile microbiome

Bacterial dynamics of the plastisphere microbiome exposed to sub-lethal antibiotic pollution – Brune Jounnard & Concepcion Sanchez-Cid – BMC Microbiome

Exploring potential polysaccharide utilization loci involved in the degradation of typical marine seaweed polysaccharides by Bacteroides thetaiotaomicron – Biao Yu – Frontiers in Microbiology

Organic matter degradation in the deep, sulfidic waters of the Black Sea: insights into the ecophysiology of novel anaerobic bacteria – Subhash Yadav – BMC Microbiome

May 17, 2024

Posted on by

Today’s digest features bioinformatics binning methods, healthy dogs, lakes in South Africa, and more. For the human gut microbiome studies, check out the latest digest (May 15, 2024) by Grace Deitzler.

See you at #MVIF!

Skin microbiome

Intraspecies warfare restricts strain coexistence in human skin microbiomes – Christopher P. Mancuso – bioRxiv

Oral microbiome

Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study – Memduh Bingöl – Journal of Clinical Periodontology

Urinary microbiome

Microbroth dilution method for antibiotic susceptibility testing of fastidious and anaerobic bacteria of the urinary microbiome – Wilson Geaman – Microbiology Spectrum

Respiratory tract

Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease – Nick Quinn-Bohmann – BMC Biology

Food microbiome

Microbial community structure of plant-based meat alternatives – Franz-Ferdinand Rochn – pj Science of Food

Plan, root, soil

Functional team selection: a framework for local adaptation in plants and their belowground microbiomes – Nancy Collins Johnson and César Marín – ecoevoRxiv

Life on the edge: microbial diversity, resistome, and virulome in soils from the Union Glacier cold desert – Patricio Arros – bioRxiv

Animal microbiome

Microbiota of healthy dogs demonstrate a significant decrease in richness and changes in specific bacterial groups in response to supplementation with resistant starch, but not psyllium or methylcellulose, in a randomized cross-over trial – Silke Salavati Schmitz – Access Microbiology

Early-life factors shaping the gut microbiota of Common buzzard nestlings – Hugo Pereira – Animal Microbiome

Animal experiment

13C-Stable isotope resolved metabolomics uncovers dynamic biochemical landscape of gut microbiome-host organ communications in mice – Xia Xiao – Microbiome

Water microbiome

Metagenomics datasets of water and sediments from eutrophication-impacted artificial lakes in South Africa – Grace Nkechinyere Ijoma – Scientific Data

Bioinformatics

Fairy: fast approximate coverage for multi-sample metagenomic binning – Jim Shaw and Yun William Yu – bioRxiv

Highly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods – Daniel M Portik – biorXiv

Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level – Amy S Graham – bioRxiv

Full factorial construction of synthetic microbial communities – Juan Diaz-Colunga – bioRxiv

ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences – Yao Pei – Microbiome

May 15, 2024

Posted on by

Human gut microbiome

A shared group of bacterial taxa in the duodenal microbiota of undernourished Pakistani children with environmental enteric dysfunction – Najeeha T Iqbal – mSphere

Gut microbiota, blood metabolites, and left ventricular diastolic dysfunction in US Hispanics/Latinos – Kai Luo – BMC Microbiome

Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition – Xuanji Li – BMC Microbiome

Impact of the gut microbiome composition on social decision-making – Marie Falkenstein – PNAS Nexus

Veillonella and Bacteroides are associated with gestational diabetes mellitus exposure and gut microbiota immaturity – Fernanda Valdez-Palomares – PLOS One

[REVIEW] The neonatal gut microbiome and global health – Pinaki Panigrahi – Gut Microbes

Functional characterization of helminth-associated Clostridiales reveals covariates of Treg differentiation – Shusan Sargisan – BMC Microbiome

Vaginal microbiome

16S rRNA female reproductive microbiome investigation reveals Dalfopristin, Clorgyline, and Hydrazine as potential therapeutics for the treatment of bacterial vaginosis – Sudeepti Kulshrestha – Diagnostic Microbiology and Infectious Disease

Fecal transplant from vaginally seeded infants decreases intraabdominal adiposity in mice – Sivaranjani Namasivayam – Gut Microbes

Animal microbiome

Viruses contribute to microbial diversification in the rumen ecosystem and are associated with certain animal production traits – Ming Yan & Zhongtang Yu – BMC Microbiome

Quantitative microbiome profiling of honey bee (Apis mellifera) guts is predictive of winter colony loss in northern Virginia (USA) – David B. Carlini – Nature Scientific Reports

How do phytophagous insects affect phyllosphere fungi? Tracking fungi from milkweed to monarch caterpillar frass reveals communities dominated by fungal yeast – Ryoko Oono – Environmental Microbiology

Beneficial microbes & compounds

The gut lactic acid bacteria metabolite, 10-oxo- cis-6, trans-11-octadecadienoic acid, suppresses inflammatory bowel disease in mice by modulating the NRF2 pathway and GPCR-signaling – Miki Ando – Frotiers in Immunology

Effect of weight loss program using prebiotics and probiotics on body composition, physique, and metabolic products: longitudinal intervention study – Nayera E Hassan – Nature Scientific Reports

Origin of the neonatal gut microbiota and probiotic intervention: a randomized controlled trial – Zhe Li – Frontiers in Nutrition

Effectiveness of probiotic- and fish oil-loaded water-in-oil-in-water (W1/O/W2) emulsions at alleviating ulcerative colitis – Qingzhao Gu – Food & Function

Plant, root, and soil microbiome

Competition mode and soil nutrient status shape the role of soil microbes in the diversity–invasibility relationship – Haokun Li – Ecology and Evolution

Dynamics and drivers of fungal communities in a multipartite ant-plant association – Veronica Barrajon-Santos – BMC Biology

Quorum sensing related activities of beneficial and pathogenic bacteria have important implications for plant and human health – Anton Hartmann – FEMS Microbiology Ecology

Impacts of vegetable processing and cheese making effluent on soil microbial functional diversity, community structure, and denitrification potential of land treatment systems – Geoffrey S. Siemering – Water Environment Research

Role of Bacillus subtilis exopolymeric genes in modulating rhizosphere microbiome assembly – Caroline Sayuri Nishisaka – BMC Environmental Microbiome

The predominant lactic acid bacteria and yeasts involved in the spontaneous fermentation of millet during the production of the traditional porridge Hausa koko in Ghana – Amy Atter – BMC Microbiology

Bioinformatics & Tools

Multi-class boosting for the analysis of multiple incomplete views on microbiome data – Andrea Simeon – BMC Bioinformatics

PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome – Lara Vázquez-González – BMC Bioinformatics

Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches – Ryan Kuster – BMC Bioinformatics

May 8, 2024

Posted on by

Happy Wednesday folks, we’re halfway through the week! Today’s blog features a number of interesting articles – it was difficult to pick just a few to highlight. Read on to learn about a new study that unveils the environment-specificity of secondary successional dynamics following microbiota disruption, a review summarizing the literature on how pesticide exposure affects the microbiota-gut-brain-axis, an investigation of how host phylogeny, diet, and anthropogenic factors shape the Cetacea gut microbiome – and more!

Human Microbiome

Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort – Tzipi Braun – Nature Communications

Improvements in Gut Microbiome Composition and Clinical Symptoms Following Familial Fecal Microbiota Transplantation in a Nineteen-Year-Old Adolescent With Severe Autism – Sabine Hazan – Journal of Medical Cases

[PREPRINT] Interplay between particle size and microbial ecology in the gut microbiome – Jeffrey Letourneau – bioRxiv

Shotgun metagenomic analysis of saliva microbiome suggests Mogibacterium as a factor associated with chronic bacterial osteomyelitis – Hiroko Yahara – PLOS One

[REVIEW] Pesticide exposure and the microbiota-gut-brain axis – Rie Matsuzaki – ISME Journal

Animal Experiments

Short-term exposure to antibiotics begets long-term disturbance in gut microbial metabolism and molecular ecological networks – Yuehui Hong – BMC Microbiome

Microbial Ecology

Synthesis of recovery patterns in microbial communities across environments – Stephanie D. Jurburg – BMC Microbiome

Cooperative interactions between invader and resident microbial community members weaken the negative diversity-invasion relationship – Johanna Vendermaesen – Ecology Letters

High speciation rate of niche specialists in hot springs – Qing He – ISME Journal

Plant, root, and soil microbiome

Effects of reduced snowpack due to climate warming on abiotic and biotic soil properties in alpine and boreal forest systems – Anastasiia Kosolapova – PLOS Climate

Microbiota recovery in a chronosquences of impoverished Cerrado soils with biosolids applications – Laibin Huang – Science of the Total Environment

Melatonin promotes the recovery of apple plants after waterlogging by shaping the structure and function of the rhizosphere microbiome – Yang Cao – Plant, Cell & Environment

Antimony efflux underpins phosphorus cycling and resistance of phosphate-solubilizing bacteria in mining soils – Shengwei Liu – ISME Journal

Animal Microbiome

Antibiotic exposure alters the honeybee gut microbiota and may interfere with the honeybee behavioral caste transition – Zijing Zhang – Insect Science

Meta-analysis of the Cetacea gut microbiome: Diversity, co-evolution, and interaction with the anthropogenic pathobiome – Elena Radaelli – Science of the Total Environment

Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification – Chandlar Tsz To Tsang – Molecular Ecology

Techniques & Methodology

A perfusion host-microbe bioreactor (HMB) system that captures dynamic interactions of secreted metabolites between epithelial cells cocultured with a human gut anaerobe – Jingyun Yang – Biotechnology and Bioengineering

Stable, fluorescent markers for tracking synthetic communities and assembly dynamics – Beatriz Jorrin – BMC Microbiome

Sterile sentinels and MinION sequencing capture active soil microbial communities that differentiate crop rotations – Sonya R. Erlandson – BMC Environmental Microbiome

April 17, 2024

Posted on by

Good morning and welcome to another MicrobiomeDigest! Did you know that one group of scientists is using video games to crowdsource puzzle solutions to improve microbiome research? What a neat way to approach citizen science! On deck today we have a study about pesticide exposure and the gut microbiome, a review of the emerging field of skin microbiome-focused cosmetics, insights into the viral diversity of bats and rodents in East Africa, an editorial exploring research into microbial symbiosis through the lens of modern tools, and more.

Human microbiome

Modulation of the gut microbiome and Firmicutes phylum reduction by a nutraceutical blend in the obesity mouse model and overweight humans: A double-blind clinical trial – Victor Nehmi-Filho et al – Food Science & Nutrition

Ambient long-term exposure to organophosphorus pesticides and the human gut microbiome: an observational study – Keren Zhang et al – BMC Environmental Health

[REVIEW] Skin Deep: The Potential of Microbiome Cosmetics – Ju Hee Han & Hei Sung Kim – Journal of Microbiology

Metabolic Interaction Between Host and the Gut Microbiota During High-Fat Diet-Induced Colorectal Cancer – Chaeeun Lee et al – Journal of Microbiology

Longitudinal microbiome changes in children exposed to proton pump inhibitors – Jason Yanjia Zhang et al – Clinical and Translational Gastroenterology

High temperature and humidity in the environment disrupt bile acid metabolism, the gut microbiome, and GLP-1 secretion in mice – Song Chen et al – Nature Communications Biology

Plant, root, and soil microbiome

Exploring the interplay between the core microbiota, physicochemical factors, agrobiochemical cycles in the soil of the historic tokaj mád wine region – Judit Remenyik et al – PLOS One

[PREPRINT] Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands – Emily Bechtold et al – bioRxiv

An in-depth evaluation of metagenomic classifiers for soil microbiomes – Niranjana Rose Edwin – BMC Environmental Microbiome

Animal microbiome

Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation – Daxi Wang et al – BMC Microbiome

Association between the gut microbiome and carotenoid plumage phenotype in an avian hybrid zone – Marcella D. Baiz et al – Proceedings of the Royal Soc. of Biological Sciences

Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs – Juan M Ortiz Sanjuan et al – BMC Animal Microbiome

Integrated analysis of gut metabolome, microbiome, and exfoliome data in an equine model of intestinal injury – C.M. Whitfield-Gargile et al – BMC Microbiome

Responses of the coral reef cryptobiome to environmental gradients in the Red Sea – Rodrigo Villalobos et al – PLOS One

Microbial ecology

[EDITORIAL] Symbiosis: In search of a deeper understanding – Thomas A Richards & Nancy A Moran – PLOS Biology

Bioinformatics & techniques

Randomized feature selection based semi-supervised latent Dirichlet allocation for microbiome analysis – Namitha Pais et al – Nature Scientific Reports

Improving microbial phylogeny with citizen science within a mass-market video game – Roman Sarrazin-Gendron et al – Nature Biotechnology

April 10, 2024

Posted on by

Good morning microbiome enthusiasts! Today’s MD is on the shorter side but we still have some really interesting articles picked out for you to peruse – including a microbiome-sparing targeted P. aeruginosa compound, effective probiotics for restoring a healthy coral microbiome, and a study characterizing the microbiome of metastatic cancers in over 4,000 biopsies. Plus, don’t forget that April’s Microbiome Virtual International Forum is happening next week!

Human Microbiome

Longitudinal multi-omics analysis uncovers the altered landscape of gut microbiota and plasma metabolome in response to high altitude – Yang Han et al – BMC Microbiome

Illuminating microflora: shedding light on the potential of blue light to modulate the cutaneous microbiome – Hannah J Serrage et al – Frontiers in Cellular and Infection Microbiology

Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC – Rauf Salamzade et al – Microbial Genomics

A pan-cancer analysis of the microbiome in metastatic cancer – Thomas Battaglia et al – Cell

A Lacticaseibacillus rhamnosus secretome induces immunoregulatory transcriptional, functional and immunometabolic signatures in human THP-1 monocytes – Michael P. Jeffrey et al – Nature Scientific Reports

The oral cavity and intestinal microbiome in children with functional constipation – Monika Kwiatkowska et al – Nature Scientific Reports

Characterization of the gut bacterial and viral microbiota in latent autoimmune diabetes in adults – Casper S. Poulsen et al – Nature Scientific Reports

Colonization during a key developmental window reveals microbiota-dependent shifts in growth and immunity during undernutrition – Yadeliz A. Serrano Matos et al – BMC Microbiome

Animal models

Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice – Tatsuya Dokoshi et al – Nature Communications

A folate inhibitor exploits metabolic differences in Pseudomonas aeruginosa for narrow-spectrum targeting – Connor Chain et al – Nature Microbiology

Animal microbiome

A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience – Lauren F. Messer et al – Nature Communications

Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment – Nathalia Delgadillo-Ordoñez et al – Nature Communications Biology

Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation – Daxi Wang et al – BMC Microbiome

Plant, root & soil microbiome

Root volatiles manipulate bacterial biofilms – Waseem Raza & Gaofei Jiang – Nature Ecology & Evolution

Analysis of endophytic bacterial diversity in seeds of different genotypes of cotton and the suppression of Verticillium wilt pathogen infection by a synthetic microbial community – Chong-Die Wu et al – BMC Plant Biology

Bioinformatics & tools

Holomics – a user-friendly R shiny application for multi-omics data integration and analysis – Katharina Munk et al – BMC Bioinformatics

April 3, 2024

Posted on by

Human Microbiome

Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria – Chenhao Li et al – Cell


Small Intestine Bacterial Overgrowth is associated with increased Campylobacter and epithelial injury in duodenal biopsies of Bangladeshi children – Shah Mohammad Fahim et al – PLOS Neglected Tropical Diseases


Placental TLR recognition of salivary and subgingival microbiota is associated with pregnancy complications – Kazune Pax et al – BMC Microbiome


Ecological patterns and processes of temporal turnover within lung infection microbiota – Helen Gavillet et al – BMC Microbiome


Integrative analysis with microbial modelling and machine learning uncovers potential alleviators for ulcerative colitis – Jinlin Zhu et al – Gut Microbes


A comparative study on dietary diversity and gut microbial diversity in children with autism spectrum disorder, attention-deficit hyperactivity disorder, their neurotypical siblings, and non-related neurotypical volunteers: a cross-sectional study – Shunya Kurokawa et al – Journal of Child Psychology & Psychiatry


Disrupted gut microecology after high-dose 131I therapy and radioprotective effects of arachidonic acid supplementation – Ganghua Lu et al – European Journal of Nuclear Medicine & Molecular Imaging


Pathogen-specific alterations in intestinal microbiota precede urinary tract infections in preterm infants: a longitudinal case-control study – Luyang Hong et al – Gut Microbes



Plant, soil, and root microbiome

Soil fungal communities varied across aspects of restored grassland in former mining areas of the Qinghai-Tibet Plateau – Xioqing Li et al – PLOS One


Integrated rice-yellow catfish farming resulting in variations in the agricultural environment, rice growth performance, and soil bacterial communities – Yiran Hou et al – Environmental Science & Pollution Research


Microbial terroir: associations between soil microbiomes and the flavor chemistry of mustard (Brassica juncea) – Corinne Walsh et al – New Phytologist


Animal experiments

The gut metabolite indole-3-propionic acid activates ERK1 to restore social function and hippocampal inhibitory synaptic transmission in a 16p11.2 microdeletion mouse model – Jian Jiang et al – BMC Microbiome


[PREPRINT] Supplier-origin gut microbiomes affect host body weight and select autism-related behaviors – Zachary L. McAdams et al – bioRxiv


Water & extremophile microbiome

Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters – Cristian Villena-Alemany et al – BMC Microbiome


The distinctive weathering crust habitat of a High Arctic glacier comprises discrete microbial micro-habitats – Sara M E Rassner et al – Environmental Microbiology


Animal Microbiome

Molecular-Weight-Dependent Degradation of Plastics: Deciphering Host-Microbiome Synergy Biodegradation of High-Purity Polypropylene Microplastics by Mealworms – Lei He et al – Environmental Science & Technology


Dispersion of antimicrobial resistant bacteria in pig farms and in the surrounding environment – Daniel Scicchitano et al – BMC Animal Microbiome


Tools & techniques

[PREPRINT] rRNA Operon Improves Species-Level Classification of Bacteria and Microbial Community Analysis Compared to 16S rRNA – Sohyoung Won et al – bioRxiv

March 27, 2024

Posted on by

Built environment microbiome

Genomic, functional, and metabolic enhancements in multidrug-resistant Enterobacter bugandensis facilitating its persistence and succession in the International Space Station – Pratyay Sengupta et al – BMC Microbiome

An overview of the bacterial microbiome of public transportation systems-risks, detection, and countermeasures – Yen-Tran Ly et al – Frontiers in Public Health

Bioinformatics and computational methods

Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics – Enhui Wu et al – BMC Microbiome

Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes – Jasper van Bemmelen et al – BMC Bioinformatics

Multi-omic integration of microbiome data for identifying disease-associated modules – Efrat Muller – Nature Communications

Animal experiments

Gender affirming hormone therapy preserves skeletal maturation in young mice via the gut microbiome – Subhashis Pal et al – Journal of Clinical Investigation

Microbiota-derived indoles alleviate intestinal inflammation and modulate microbiome by microbial cross-feeding – Gang Wang et al – BMC Microbiome

[PREPRINT] Akkermansia muciniphila identified as key strain to alleviate gut barrier injury through Wnt signaling pathway – Xin Ma et al – bioRxiv

Microbiota from human infants consuming secretors or non-secretors mothers’ milk impacts the gut and immune system in mice – Manoj Gurung et al – mSystems

Plant and soil microbiome

Lose-lose consequences of bacterial community-driven invasions in soil – Xipeng Liu & Joana Falcão Salles – BMC Microbiome

Manipulating the physical distance between cells during soil colonization reveals the importance of biotic interactions in microbial community assembly – Sana Romdhane et al – BMC Environmental Microbiome

Soil fungal communities varied across aspects of restored grassland in former mining areas of the Qinghai-Tibet Plateau – Xioaqing Li et al – PLOS One

Animal microbiome

Exploring the potential effects of forest urbanization on the interplay between small mammal communities and their gut microbiota – Marie Bouilloud et al – BMC Animal Microbiome

Bats, Bacteria, and Bat Smell V.2.0: Repeatable Sex-Specific Differences in Scent Organ Microbiota – Öncü Maraci et al – Microbial Ecology

Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs – Jacoba I. Bromfield et al – mSphere

Phylosymbiosis and metabolomics resolve phenotypically plastic and cryptic sponge species in the genus Agelas across the Caribbean basin – M.S. Pankey et al – Molecular Ecology

Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition – C. E. Dubé et al – Nature Communications

March 20, 2024

Posted on by

Human gut and general microbiome

Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition – Hao-Wei Chang et al – Nature Microbiology

Outcomes after Fecal Microbiota Transplantation in combination with Bezlotoxumab for Inflammatory Bowel Disease and Recurrent C. difficile Infection – Jessica R Allegretti – American Journal of Gastroenterology

Diosmin alleviates ulcerative colitis in mice by increasing Akkermansia muciniphila abundance, improving intestinal barrier function, and modulating the NF-κB and Nrf2 pathways – Maha Badr Salem et al – Cell Heliyon

Gut microbiota profiling in obese children from Southeastern China – Jingjing Wang et al – BMC Pediatrics

A flexible high-throughput cultivation protocol to assess the response of individuals’ gut microbiota to diet-, drug-, and host-related factors – Janina N Zünd et al – ISME Communications

Animal experiments

Intact lung tissue and bronchoalveolar lavage fluid are both suitable for the evaluation of murine lung microbiome in acute lung injury – Lijun Zheng et al – BMC Microbiome

Microbiota-derived indoles alleviate intestinal inflammation and modulate microbiome by microbial cross-feeding – Gang Wang et al – BMC Microbiome

Plant, soil, and environmental microbiome

Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development – Chao Xiong et al – mSystems

Bacterial communities associated with an island radiation of lichen-forming fungi – Miguel Blázquez et al – PLOS ONE

Built environment microbiome

Early assessment of fungal and oomycete pathogens in greenhouse irrigation water using Oxford nanopore amplicon sequencing – Enoch Narh Kudjordjie et al – PLOS One

The composition of the bacterial communities collected from the PM10 samples inside the Seoul subway and railway station – Shambhavi Sharma et al – Nature Scientific Reports

Bioinformatics

Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values – Seungjun Ahn & Somnath Datta – BMC Bioinformatics

Beneficial microbes & microbial metabolites
Natural intestinal metabolite xylitol reduces BRD4 levels to mitigate renal fibrosis – Zhouke Tan et al – Clinical and Translational Science

Probiotics supplementation during pregnancy or infancy on multiple food allergies and gut microbiota: a systematic review and meta-analysis – Lan Jiang et al – Nutrition Reviews

Non-Microbiome Microbiology

Koch’s curse: How models of extreme pathology bias studies of host–pathogen interactions – Kalyan K. Dewan & Eric T. Harvill – PLOS Pathogens

March 13, 2024

Posted on by

Human gut microbiome

Gut microbiota–tryptophan metabolism–GLP-1 axis participates in β-cell regeneration induced by dapagliflozin – Yafei Jiang et al – Diabetes

Inhibition of inosine metabolism of the gut microbiota decreases testosterone secretion in the testis – Lei Tang et al – mSystems

[REVIEW] Exploring the gut microbiota and its potential as a biomarker in gliomas – Dana Aljarrah et al – Biomedicine & Pharmacotherapy

Comparative prebiotic potential of galacto- and fructo-oligosaccharides, native inulin and acacia gum in Kenyan infant gut microbiota during iron supplementation – Paula Momo Cabera et al – ISME Communications

A bacterial sialidase mediates early-life colonization by a pioneering gut commensal – Ekaterina Buzun et al – Cell Host and Microbe

Animal Microbiome

Dietary carbohydrate sources differently prime the microbial ecosystem but not the epithelial gene expression profile along the complete gut of young calves – Thomas Hartinger et al – BMC Animal Microbiome

Multi-omics reveals that alkaline mineral water improves the respiratory health and growth performance of transported calves – Jiancheng Qi et al – BMC Microbiome

Efficacy of a novel multi-enzyme feed additive on growth performance, nutrient digestibility and gut microbiome of weanling pigs fed corn-wheat or wheat-barley based diet – Ayodeji S Aderibigbe et al – Journal of Animal Science

Plant and soil microbiome

Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition – Jia Wang et al – mSystems

Plasma Treatment Modifies Element Distribution in Seed Coating and Affects Further Germination and Plant Growth through Interaction with Soil Microbiome – Tetiana Kalachova et al – Journal of Agricultural and Food Chemistry

Soil Microbiomes and their Arsenic Functional Genes in Chronically High-Arsenic Contaminated Soils – Prinpida Sonthiphand et al – Bulletin of Environmental Contamination and Toxicology

Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria – Katarina Hrovat et al – ISME Communications

Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process – Liqun Jiang et al – Microbiology Spectrum

Diversity and distribution of biosynthetic gene clusters in agricultural soil microbiomes – Ziguo Zhang et al – mSystems

Sugar transporters spatially organize microbiota colonization along the longitudinal root axis of Arabidopsis – Eliza P.-I. Loo et al – Cell Host and Microbe

Built environment microbiome

Microbiome analysis of the restricted bacteria in radioactive element-containing water at the Fukushima Daiichi Nuclear Power Station – Tomoro Warashina et al – Applied and Environmental Microbiology

Bioinformatics and Techniques

The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes – Thibaut Dumas et al – BMC Microbiome

Proportion-based normalizations outperform compositional data transformations in machine learning applications – Aaron Yerke et al – BMC Microbiome

A method to correct for local alterations in DNA copy number that bias functional genomics assays applied to antibiotic-treated bacteria – Geraldine J. Sullivan et al – mSystems

[PREPRINT] Bacterial strain nomenclature in the genomic era: Life Identification Numbers using a gene-by-gene approach – Federica Palma et al – bioRXiv