August 16, 2022

Human and General Microbiome

Crohn’s disease in endoscopic remission, obesity, and cases of high genetic risk demonstrates overlapping shifts in the colonic mucosal-luminal interface microbiome – Jonathan P Jacobs – Genome Medicine

Preservation of fecal microbiome is associated with reduced severity of Graft-versus-Host Disease – Marina Burgos da Silva – Blood

Cobamide Sharing Is Predicted in the Human Skin Microbiome – Mary Hannah Swaney – mSystems

Postnatal exposure to ambient air pollutants is associated with the composition of the infant gut microbiota at 6-months of age – Maximilian J Bailey – Gut Microbes

Shotgun metagenomic sequencing reveals skin microbial variability from different facial sites – Qingzhen Wei – Frontiers in Microbiology

Review: Recent insights into the role of microbiome in the pathogenesis of obesity – Eduard W J van der Vossen – Therapeutic Advances in Gastroenterology

Model Animal Microbiome

Impact of habitual chewing on gut motility via microbiota transition – Fukie Yaoita – Scientific Reports

Resources to Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model to Study Microbiome Function – Alexandra Proctor – mSystems

Non-model Animal Microbiome

The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate – David M Needham – Nature Microbiology

Characterization of presence and activity of microRNAs in the rumen of cattle hints at possible host-microbiota cross-talk mechanism – Sara Ricci – Scientific Reports

Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts – Min Hui – PeerJ

Systematic profiling of the chicken gut microbiome reveals dietary supplementation with antibiotics alters expression of multiple microbial pathways with minimal impact on community structure – Angela Zou – Microbiome

Environmental Microbiome

Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction – Alessandro Rossi – Microbiome

Food Microbiome

Microbiome and Metabiotic Properties of Kefir Grains and Kefirs Based on Them –  Ding Fan – Microbiology

Profiling the role of microorganisms in quality improvement of the aged flue-cured tobacco – Xinying Wu – BMC Microbiology

August 13, 2022

Human and General Microbiome

Integrated metagenomic and metabolomic analysis reveals distinct gut-microbiome-derived phenotypes in early-onset colorectal cancer – Cheng Kong – Gut

A decrease in functional microbiomes represented as Faecalibacterium affects immune homeostasis in long-term stable liver transplant patients – Soon Kyu Lee – Gut Microbes

Longitudinal study of the vaginal microbiome in pregnancies involving preterm labor – Yoshiko Sakabe – Fujita Medical Journal

Oral microbiome and serological analyses on association of Alzheimer’s disease and periodontitis – Kuan-Lun Fu – Oral Diseases

Review: Ultra-processed foods and human health: from epidemiological evidence to mechanistic insights – Bernard Srour – The Lancet. Gastroenterology & Hepatology

Beneficial Microbes, Compounds and Interventions

Dietary Fiber Modulates the Release of Gut Bacterial Products Preventing Cognitive Decline in an Alzheimer’s Mouse Model – Daniel Cuervo-Zanatta – Cellular and Molecular Neurobiology

Functional and safety characterization of beneficial vaginal lactic acid bacteria for the design of vaginal hygiene products – Jessica Alejandra Silva – Journal of Applied Microbiology

Butyrate-producing Eubacterium rectale suppresses lymphomagenesis by alleviating the TNF-induced TLR4/MyD88/NF-κB axis – Haiyang Lu – Cell host & Microbe

Review: The double-edged sword of probiotic supplementation on gut microbiota structure in Helicobacter pylori management – Ali Nabavi-Rad – Gut Microbes

Non-Model Animal Microbiome

Functional Redundancy in Bat Microbial Assemblage in the Presence of the White Nose Pathogen – Matthew Grisnik – Microbial Ecology

Non-steroidal anti-inflammatory drugs caused an outbreak of inflammation and oxidative stress with changes in the gut microbiota in rainbow trout (Oncorhynchus mykiss) – N Hodkovicova – The Science of the Total Environment

Bees under interactive stressors: The novel insecticides flupyradifurone and sulfoxaflor along with the fungicide azoxystrobin disrupt the gut microbiota of honey bees and increase opportunistic bacterial pathogens – Yahya Al Naggar – The Science of the Total Environment

Plant Microbiome

Host genotype controls ecological change in the leaf fungal microbiome – Acer VanWallendael – PLoS Biology

Suaeda salsa Root-Associated Microorganisms Could Effectively Improve Maize Growth and Resistance under Salt Stress – Yongdong Wang – Microbiology Spectrum

Review: Regulation of immune complex formation and signalling by FERONIA, a busy goddess in plant-microbe interactions – Zhikun Duan – Molecular Plant Pathology

Food Microbiome

A systematic, complexity-reduction approach to dissect the kombucha tea microbiome – Xiaoning Huang – eLife

Bioinformatic Tools and Microbiome Analysis Techniques

ProbeTools: designing hybridization probes for targeted genomic sequencing of diverse and hypervariable viral taxa – Kevin S Kuchinski – BMC Genomics

A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications – Maaly Nassar – GigaScience

MetaProClust-MS1: an MS1 Profiling Approach for Large-Scale Microbiome Screening – Caitlin M A Simopoulos – mSystems

August 6, 2022

Human and General Microbiome

The oral microbiome and lung cancer risk: An analysis of 3 prospective cohort studies – Emily Vogtmann – Journal of the National Cancer Institute

Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries – M J Carvalho – Nature Microbiology

Crosstalk between mucosal microbiota, host gene expression, and sociomedical factors in the progression of colorectal cancer – Namjoo Kim – Scientific Reports

Using Culture-Enriched Phenotypic Metagenomics for Targeted High-Throughput Monitoring of the Clinically Important Fraction of the β-Lactam Resistome – Zhiguo Zhang – Environmental Science & Technology

Review: Porphyromonas gingivalis and dental stem cells crosstalk amplify inflammation and bone loss in the periodontitis niche – Devaraj Ezhilarasan – Journal of Cellular Physiology

Beneficial Microbes and Compounds

On the effect of flavonoids and dietary fibre in lingonberries on atherosclerotic plaques, lipid profiles and gut microbiota composition in Apoe(-/-) mice – Jiyun Liu – International Journal of food Sciences and Nutrition

The Gut-Brain-Microbiome Connection: Can Probiotics Decrease Anxiety and Depression? – Jennifer Maybee – Issues in Mental Health Nursing

The effect of Lactobacillus rhamnosus B10 on alcoholic liver injury and intestinal microbiota in alcohol-induced mice model – Xia Li – Journal of Food Biochemistry

Model Animal Microbiome

The effect of young blood plasma administration on gut microbiota in middle-aged rats – Taha Ceylani – Archives of Microbiology

Non-Model Animal Microbiome

Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus – Aleksandra I Krawczyk – Microbiome

Host taxonomy determines the composition, structure, and diversity of the earthworm cast microbiome under homogenous feeding conditions – Manuel Aira – FEMS Microbiology Ecology

Ruminal Microbiota Determines the High-Fiber Utilization of Ruminants: Evidence from the Ruminal Microbiota Transplant – Xiaodong Chen – Microbiology Spectrum

Bioinformatics and Microbiome Analysis Techniques

Computational approach to modeling microbiome landscapes associated with chronic human disease progression – Lu Li – PLoS Computational Biology

Guideline for the analysis of the microbial communities of the human upper airways – Leonardo Mancabelli – Journal of Oral Microbiology

August 1st, 2022

God morgon!

Good morning from Sweden.

Today’s digest has studies from diverse topics but the one that caught my attention is a preprint that addresses the controversial question of presence of a ‘normal blood microbiota’ in humans. The authors of this preprint analysed about 10,000 humans samples and provide evidence that there is no core blood microbiota.

A new preprint describes a unique Taleocin (a bacteriocin) from Pseudomonas syringae which defies the convention that bacteriocins have a narrow spectrum. The bacteriocin has a broad range killing activity against agriculturally important pathogens like Erwinia amylovora and Xanthomonas perforans as well as against the clinical human pathogen Salmonella choleraesuis.

Another preprint reports metabolic interactions responsible for unusually high Iron and lipid content in Geobacter sulfurreducens, a bacterium known iron reducing bacterium in the soil. Another environmental study found that human pathogens are the major carriers of antibiotic resistance genes in the Yangtze river – one of the longest in the world. This is in contrast to prevalent belief that conventional supercarriers are Enterococcus spp. and other fecal indicator bacteria.

Elsewhere in the digest is a preprint from my previous lab where my old colleagues have reported a small RNA and metal dependent mechanism that regulates the survival of Acinetobacter baumannii under oxidative stress.

As a bonus, there is a super intriguing preprint where the authors have actually provided evidence that coming up with creative and funny titles for your papers can help them gain more visibility and citations! So, all of you writing an article or planning to write one soon, this is a great tip!

I hope you will enjoy reading today’s digest and have a great week ahead!

Human gut

Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake – Zachary C. Holmes, et al., Microbiome

Near-sterile sites

Preprint: No evidence for a common blood microbiome based on a population study of 9,770 healthy humans – Cedric C.S. Tan, et al.

Water microbiome

Supercarriers of antibiotic resistome in a world’s large river – Jiawen Wang, et al., Microbiome

Oceanospirillales containing the DMSP lyase DddD are key utilisers of carbon from DMSP in coastal seawater – Jingli Liu, et al., Microbiome

Community structure of coral microbiomes is dependent on host morphology – Kathleen M. Morrow, et al., Microbiome

Preprint: The impact of primary colonizers on the community composition of river biofilm – Roshan Angoshtari, et al.

Soil microbiome

Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity – Xingyu Ma, et al., Microbiome

Animal microbiome

Host-microbiota interaction-mediated resistance to inflammatory bowel disease in pigs – Xuan Zhao, et al., Microbiome

Preprint: The differing roles of flavins and quinones in extracellular electron transfer in Lactiplantibacillus plantarum – Joe Gregory Tolar, et al.

Bacteria Hysteria

Preprint: Interspecies Killing Activity of Pseudomonas syringae Tailocins – Savannah L Weaver, et al.

Preprint: Enhanced production of natural shiga toxin by overexpressing A subunit of Stx2e in Stx2e-producing Escherichia coli isolated in South Korea – Jin Hur, et al.

Preprint: Geobacter sulfurreducens′ unique metabolism results in cells with a high iron and lipid content – Ethan T Howley, et al.

Preprint: Cloning, heterologous expression and characterization of o-phthalyl-CoA decarboxylase from phthalate degrading denitrifying bacterium – Madan Junghare

Preprint: Acinetobacter baumannii defends against oxidative stress through a Mn2+-dependent small RNA-mediated suppression of type VI secretion system – Somok Bhowmik, et al.

Techniques

Preprint: Programmable acetylation modification of bacterial proteins by a Cas12a-guided acetyltransferase – Liu yanqiang, et al.

Fun

Preprint: If this title is funny, will you cite me? Citation impacts of humour and other features of article titles in ecology and evolution – Stephen B Heard, et al.

July 30, 2022

Have a nice weekend! Today, the Digest contains several reviews.

Highlights!

Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake – Zachary C Holmes – Microbiome → A three-way crossover study showed that prebiotic personalization regimens can be beneficial in different manners to different people; this study showed that people with low fiber intake received more effect from those interventions.

Human and General Microbiome

Differential Gut Microbiota Compositions Related With the Severity of Major Depressive Disorder – Qi Zhong – Frontiers in Cellular and Infection Microbiology

Phospholipid metabolites of the gut microbiota promote hypoxia-induced intestinal injury via CD1d-dependent γδ T cells – Yuyu Li – Gut Microbes

Gut bacteria interact directly with colonic mast cells in a humanized mouse model of IBS – Chiko Shimbori – Gut Microbes

Asthma and Wheeze Severity and the Oropharyngeal Microbiota in Children and Adolescents – Jonathan Thorsen – Annals of the American Thoracic Society

Minireview: Role of microbial secreted proteins in gut microbiota-host interactionsBoris Vidal-Veuthey – Frontiers in Cellular and Infection Microbiology 

Review: A Bibliometric Analysis of Research on the Links Between Gut Microbiota and Atherosclerosis – Ya Wang – Frontiers in Cardiovascular Medicine

Review: Microbiota-derived metabolites as drivers of gut-brain communication – Hany Ahmed – Gut Microbes

Review: Female reproductive dysfunctions and the gut microbiota – Sangappa B Chadchan – Journal of Molecular Endocrinology

Systematic Review: A Bibliometric Review on Gut Microbiome and Alzheimer’s Disease Between 2012 and 2021 – Alejandro I Trejo-Castro – Frontiers in Aging Neuroscience

Systematic Review: Disturbances of Vaginal Microbiome Composition in Human Papillomavirus Infection and Cervical Carcinogenesis: A Qualitative Systematic Review – Ming Wu – Frontiers in Oncology

Beneficial Microbes and Compounds

Review: Bacterial-fungal metabolic interactions within the microbiota and their potential relevance in human health and disease: a short review – Alexia Lapiere – Gut Microbes

Animal Model Microbiome

Intestinal Inflammation Reversibly Alters the Microbiota to Drive Susceptibility to Clostridioides difficile Colonization in a Mouse Model of Colitis – Madeline R Barron – mBio

Non-Model Animal Microbiome

Comparative and functional analyses of fecal microbiome in Asian elephants – Guiding Li – Antonie van Leeuwenhoek

Bioinformatics and Microbiome Analysis Techniques

Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake – Luke R Thompson – GigaScience

July 26, 2022

Highlights!

Microbial determinants of effective donors in faecal microbiota transplantation for UC – Craig Haifer – Gut → Metagenomic and metabolomic data analysis showed that donor microbiota stability and increased species evenness were identified novel markers associated with donor sample therapeutic efficacy in Ulcerative Colitis.

A gut microbial peptide and molecular mimicry in the pathogenesis of type 1 diabetes – Khyati Girdhar – PNAS → A peptide sequence from Parabacteroides distasonis mimics an important insulin epitope, making it susceptible to generating type I diabetes in a mouse model. 

Human and General Microbiome

Gut microbiome changes in anti-N-methyl-D-aspartate receptor encephalitis patients – Jingya Wei – BMC Neurology

Effect of a bacteriocin-producing Streptococcus salivarius on the pathogen Fusobacterium nucleatum in a model of the human distal colon – Garreth W Lawrence – Gut Microbes

Identification of Gut Microbiome Metabolites via Network Pharmacology Analysis in Treating Alcoholic Liver Disease – Ki-Kwang Oh – Current Issues in Molecular Biology

Review: The Gut Microbiota: A Double Edge Sword in Endometriosis – Chandni Talwar – Biology of Reproduction

Non-Model Animal Microbiome

Hair Microbiome Diversity within and across Primate Species – Catherine Kitrinos – mSystems

Seasonal variations in the composition and diversity of gut microbiota in white-lipped deer (Cervus albirostris) – Zhangqiang You – PeerJ

Plant Microbiome

Effects of Domestication on Plant-Microbiome Interactions – Andres Gutierrez – Plant & Cell Physiology

Evaluation of protein extraction methods for metaproteomic analyses of root-associated microbes – Fernanda Salvato – Molecular Plant-Microbe Interactions

Environmental Microbiome

Absence of stress-promoted facilitation coupled with a competition decrease in the microbiome of ephemeral saline lakes – Mateu Menéndez-Serra – Ecology

Insights into the Antimicrobial Activities and Metabolomes of Aquimarina (Flavobacteriaceae, Bacteroidetes) Species from the Rare Marine Biosphere – Sandra Godinho Silva – Marine Drugs

More microbes

Correspondence: International travel, the gut microbiome, and ESBL-E coli carriage – Ye Peng – The Lancet. Microbe

An Engineered λ Phage Enables Enhanced and Strain-Specific Killing of Enterohemorrhagic Escherichia coli – Menglu Jin – Microbiology Spectrum

Bioinformatics and Microbiome Analysis Techniques

MOCHI, a comprehensive cross-platform tool for amplicon-based microbiota analysis – Jun-Jie Zheng – Bioinformatics

July 23, 2022

Greetings from Chile! Today, in this Digest, a variety of papers covering different subjects, such as the relationships between microbiome and C. difficile infection, new skin microbiome sampling techniques, FMT donor-recipient microbiome interplay, microbiome and biodiversity conservation, microbiome and vitamin metabolism, etc.; also, take a look at the papers from the “Bioinformatics and Microbiome Analysis Techniques” section.  

Human and General Microbiome

A 3D-printed transepidermal microprojection array for human skin microbiome sampling – Kun Liang – PNAS

Analysis of Intestinal Mycobiota of Patients with Clostridioides difficile Infection among a Prospective Inpatient Cohort – Yangchun Cao – Microbiology Spectrum

Role of gastrointestinal microbial populations, a terra incognita of the human body in the management of intestinal bowel disease and metabolic disorders – J E Vazquez Bucheli – Beneficial Microbes

The Gut Bacterial Community Potentiates Clostridioides difficile Infection Severity – Nicholas A Lesniak – mBio

The interplay of gut microbiota between donors and recipients determines the efficacy of fecal microbiota transplantation – Ruiqiao He – Gut Microbes

Gut commensals expand vitamin A metabolic capacity of the mammalian host – Maryam Bonakdar – Cell Host & Microbe

A reappraisal of microbiome dysbiosis during experimental periodontitis – Marion Arce – Molecular Oral Microbiology

Activity-based protein profiling identifies alternating activation of enzymes involved in the bifidobacterium shunt pathway or mucin degradation in the gut microbiome response to soluble dietary fiber – Bryan J Killinger – NPJ Biofilms and Microbiomes

Cooperative action of gut-microbiota-accessible carbohydrates improves host metabolic function – Sawako Tomioka – Cell Reports

Model Animal Microbiome

Key features of the genetic architecture and evolution of host-microbe interactions revealed by high-resolution genetic mapping of the mucosa-associated gut microbiome in hybrid mice – Shauni Doms – eLife

Non-Model Animal Microbiome

Metagenomic insights into the microbe-mediated B and K(2) vitamin biosynthesis in the gastrointestinal microbiome of ruminants – Qian Jiang – Microbiome

Exploring the Transient Microbe Population on Citrus Butterfly Wings – P D Kamala Jayanthi – Microbiology Spectrum

Review: Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter – Júnia Schultz – mSystems

Plant Microbiome

Plant genetic effects on microbial hubs impact host fitness in repeated field trials – Benjamin Brachi – PNAS

Review: Beneficial and pathogenic plant-microbe interactions during flooding stress – Clara Martínez-Arias – Plant, Cell & Environment

Environmental Microbiome

Review: Harnessing the microbiome to prevent global biodiversity loss – Raquel S Peixoto – Nature Microbiology

More Microbes

Proteome Exploration of Legionella pneumophila To Identify Novel Therapeutics: a Hierarchical Subtractive Genomics and Reverse Vaccinology Approach – Md Tahsin Khan – Microbiology Spectrum

Bioinformatics and Microbiome Analysis Techniques

LOCOM: A logistic regression model for testing differential abundance in compositional microbiome data with false discovery rate control – Yingtian Hu – PNAS

A metagenomic DNA sequencing assay that is robust against environmental DNA contamination – Omary Mzava – Nature Communications

Bioinformatic Analysis to Investigate Metaproteome Composition Using Trans-Proteomic Pipeline – Steven He – Current Protocols

July 19, 2022

Have a nice Tuesday! Today in this short digest, interesting reviews about “psychobiotics” (useful probiotics for mental health), the use of several tools for analyzing microbiota, and a systematic review analyzing the role of the oral microbiome in autoimmune diseases. 

Human and General Microbiome

The relationship between the gut microbiome and the risk of respiratory infections among newborns – Yuka Moroishi – Communications Medicine

Review: Psychobiotics: the Influence of Gut Microbiota on the Gut-Brain Axis in Neurological Disorders – Parvin Oroojzadeh – Journal of Molecular Neuroscience

Review: Ecosystem-specific microbiota and microbiome databases in the era of big data – Victor Lobanov – Environmental Microbiome

Systematic Review: The Oral Microbiome and Its Role in Systemic Autoimmune Diseases: A Systematic Review of Big Data Analysis – Lu Gao – Frontiers in Big Data

Animal Model Microbiome

Microplastics-perturbed gut microbiota triggered the testicular disorder in male mice: Via fecal microbiota transplantation – Siyue Wen – Environmental Pollution

Plant Microbiome

Flavonoid-attracted Aeromonas sp. from the Arabidopsis root microbiome enhances plant dehydration resistance – Danxia He – The ISME Journal

Bioinformatics and Microbiome Analysis Techniques

ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics – Po Lam Chan – Database

A structural metagenomics pipeline for examining the gut microbiome – Morgan E. Walker – Current Opinion in Structural Biology 

The Mini Colon Model: a benchtop multi-bioreactor system to investigate the gut microbiome – Zijie Jin – Gut Microbes

July 16, 2022

Human and General Microbiome

Advances and challenges in cataloging the human gut virome – Junhua Li – Cell Host & Microbe

Genomic diversity of genus Limosilactobacillus – Magdalena Ksiezarek – Microbial Genomics

Comparison of the respiratory tract microbiome in hospitalized COVID-19 patients with different disease severity – Jiali Chen – Journal of Medical Virology

An international report on bacterial communities in esophageal squamous cell carcinoma – Jason Nomburg – International Journal of Cancer

Beneficial Microbes and Compounds

Phenolic-rich beverages reduce bacterial TMA formation in an ex vivo-in vitro colonic fermentation model – Lisard Iglesias-Carres – Food & Function

Lactobacillus paragasseri OLL2809 Improves Depression-Like Behavior and Increases Beneficial Gut Microbes in Mice – Narumi Hashikawa-Hobara – Frontiers in Neuroscience

In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus – Linda B Oyama – NPJ Biofilms and Microbiomes

Review: How Dietary Fibre, Acting via the Gut Microbiome, Lowers Blood Pressure – Chudan Xu – Current Hypertension Reports

Review: Low FODMAP diet in irritable bowel syndrome: a review of recent clinical trials and meta-analyses – Kevin Whelan – Current Opinion in Clinical Nutrition and Metabolic Care

Review: Prebiotic effects of plant-derived (poly)phenols on host metabolism: Is there a role for short-chain fatty acids? – Perla Lopes de Freitas – Critical Reviews in Food Science and Nutrition

Animal Microbiome

Unveiling biogeographic patterns in the worldwide distributed Ceratitis capitata (medfly) using populations genomics and microbiome composition – María Belén Arias – Molecular Ecology

Differential oral microbiome in nonhuman primates from periodontitis susceptible and resistant matrilines – Jeffrey L Ebersole – Molecular Oral Microbiology

Chicken jejunal microbiota improves growth performance by mitigating intestinal inflammation – Xiaolong Zhang – Microbiome

Bioinformatics and Microbiome Analysis

Comparison Analysis of Different DNA Extraction Methods on Suitability for Long-Read Metagenomic Nanopore Sequencing – Lei Zhang – Frontiers in Cellular and Infection Microbiology

KOMB: K-core based de novo characterization of copy number variation in microbiomes – Advait Balaji – Computational and Structural Biotechnology Journal

CASPER: An Integrated Software Platform for Rapid Development of CRISPR Tools – Brian Mendoza – The CRISPR Journal

Integrating Choline and Specific Intestinal Microbiota to Classify Type 2 Diabetes in Adults: A Machine Learning Based Metagenomics Study – Qiang Zeng – Frontiers in Endocrinology

July 12, 2022

Human and General Microbiome

Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections – Paula Hayakawa Serpa – Genome Medicine

Alterations in gut microbiota of esophageal squamous cell carcinoma patients – Man Kit Cheung – Journal of Gastroenterology and Hepatology

Altered Pattern of Immunoglobulin A-Targeted Microbiota in Inflammatory Bowel Disease After Fecal Transplantation – Wen-Qi Huang – Frontiers in Microbiology

16S rRNA gene sequencing reveals an altered composition of gut microbiota in children with Mycoplasma pneumoniae pneumonia treated with azithromycin – Qiong Deng – The Journal of General and Applied Microbiology

Clinical and metagenomic profiling of hormonal acne-prone skin in different populations – Nina Hrapovic – Journal of Cosmetic Dermatology

Microbiota diversity in nonalcoholic fatty liver disease and in drug-induced liver injury – Cristina Rodriguez-Diaza – Pharmacological Research

Beneficial Microbes and Compounds

Review: The potential role of prebiotics, probiotics, and synbiotics in adjuvant cancer therapy especially colorectal cancer – Zahoor Alam – Journal of Food Biochemistry

Review: Probiotics, prebiotics and postbiotics for better sleep quality: a narrative review – J E Haarhuis – Beneficial Microbes

Review: Gut Microbiota: A Novel Therapeutic Target for Parkinson’s Disease – Manlian Zhu – Frontiers in Immunology

Animal Model Microbiome

Obesity enriches for tumor protective microbial metabolites and treatment refractory cells to confer therapy resistance in PDAC – Kousik Kesh – Gut Microbes

Profiling of d-alanine production by the microbial isolates of rat gut microbiota – Cindy J. Lee – The FASEB Journal

Non-Model Animal Microbiome

Within-community variation of interspecific divergence patterns in passerine gut microbiota – Jan Kubovčiak – Ecology and Evolution

Bacteriophages

Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria – Brian Y. Hsueh – Nature Microbiology

Bioinformatics and Microbiome Analysis

Preprint: CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning – Alex Chklovski – biorXiv

Cancer type classification using plasma cell-free RNAs derived from human and microbes – Shanwen Chen – eLife

Temporal Alignment of Longitudinal Microbiome Data – Ran Armoni – Frontiers in Microbiology

A Bottom-up Approach to Testing Hypotheses That Have a Branching Tree Dependence Structure, with Error Rate Control – Yunxiao Li – Journal of the American Statistical Association