July 18, 2020

Have a nice weekend! Today, in this Digest: microbiome in psoriasis, cancer and a set of papers about vaginal microbiome.  

Human and General Microbiome

The cutaneous and intestinal microbiome in psoriatic disease – Stephanie T. Lea – Clinical Immunology

Microbiome-induced antigen presenting cell recruitment coordinates skin and lung allergic inflammation – Niki D. Ubags – Journal of Allergy and Clinical Immunology

Butyrate, but not Propionate, Reverses Maternal Diet-Induced Neurocognitive Deficits in Offspring – Linchao Yu – Pharmacological Research

Host Genotype and Colonist Arrival Order Jointly Govern Plant Microbiome Composition and Function – Devin R. Leopold – Current Biology

Characterization of gut contractility and microbiota in patients with severe chronic constipation – Dina R. Yarullina – PLoS ONE

A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron – Daniel Ryan – Nature Communications 

Bacteria pathogens drive host colonic epithelial cell promoter hypermethylation of tumor suppressor genes in colorectal cancer – Xiaoxuan Xia – Microbiome

Vaginal microbiome analysis of healthy women during different periods of gestation – Dan Li – Bioscience Reports

The Gut Microbiome as a Component of the Gut-Brain Axis in Cognitive Health – Wen Gao – Biological Research For Nursing 

The Effect of Gut Microbiome on Carcinogenic DNA Damage – Yun-Chung Hsiao – Chemical Research in Toxicology

The effect of curative resection on fecal microbiota in patients with colorectal cancer: a prospective pilot study – Sung Sil Park – Annals of Surgical Treatment and Research

Tumor microbial diversity and compositional differences among women in Botswana with high-grade cervical dysplasia and cervical cancer – Travis T Sims – International Journal of Gynecological Cancer

Gut microbial composition changes in bladder cancer patients: A case-control study in Harbin, China – Canxia He –  Asia Pacific Journal of Clinical Nutrition

Beneficial Microbes, Interventions, and Compounds

A 4-strain Probiotic Supplement Influences Gut Microbiota Composition and Gut Wall Function in Patients with Ulcerative Colitis – Jonas Ghyselinck – International Journal of Pharmaceutics

Systematic Review: Probiotics for induction of remission in Crohn’s disease – Berkeley N Limketkai – Cochrane Systematic Review

Human milk and mucosa-associated disaccharides impact on cultured infant fecal microbiota – Antonio Rubio-del-Campo – Scientific Reports 

YYFZBJS ameliorates colorectal cancer progression in ApcMin/+ mice by remodeling gut microbiota and inhibiting regulatory T-cell generation – Hua Sui – Cell Communication and Signaling 

Challenges of Screening Prospective Stool Donors for Fecal Microbiota Transplantation – Nancy E. Dubois – Biological Research For Nursing

Effects of banana powder (Musa acuminata Colla) on the composition of human fecal microbiota and metabolic output using in vitro fermentation – Dan‐Dan Tian – Journal of Food Science

COVID-19 Papers

ACE2 and TMPRSS2 expression by clinical, HLA, immune, and microbial correlates across 34 human cancers and matched normal tissues: implications for SARS-CoV-2 COVID-19 – Riyue Bao – Journal of ImmunoTheraphy of Cancer

July 4, 2020

Greetings from Santiago, Chile! Today in this Digest, we have studies about the influence of alcohol use disorder on the microbiota, several papers about the influence of different compounds (from allicin to DAV132, a colon-targeted antibiotic adsorbent) on the microbiota. Today we have several papers about different models of plant- or soil- associated microbiomes, and a couple of papers from studies with SIV infection models. Have a nice weekend!

Human and General Microbiome

Longitudinal gut microbiome changes in alcohol use disorder are influenced by abstinence and drinking quantity – Nancy Ames et al., Gut Microbes

Comparative evaluation of peptidome and microbiota in different types of saliva samples – Ce Zhu et al.,Annals of Translational Medicine

Preprint: Microbial control over host diet selection – Brian K Trevelline and Kevin D Kohl – BioRxiv

Functional Compounds and the Microbiome

Hemolysin BL from novel Bacillus toyonensis BV-17 induces antitumor activity both in vitro and in vivo – Jiajia Chen et al., Gut Microbes

Modeling the effect of DAV132, a novel colon-targeted adsorbent, on fecal concentrations of moxifloxacin and gut microbiota diversity in healthy volunteers – Jinju Guk et al.,Clinical Pharmacology and Therapeutics

Allicin-induced host-gut microbe interactions improves energy homeostasisChuanhai Zhang et al., – The FASEB Journal

Evidence of Microbiome-Drug Interactions between the Antimalarial Lumefantrine and Gut Microbiota in Mice – Matthew M. Ippolito et al., The American Society of Tropical Medicine and Hygiene

Contrasting effects of viscous and particulate fibers on colonic fermentation in vitro and in vivo, and their impact on intestinal water studied by MRI in a randomized trial – David Gunn et al., The American Journal of Clinical Nutrition

Animal Microbiome / Animal Models

A theoretic approach to the mode of gut microbiome translocation in SIV-infected Asian macaques – Wendy Li and Zhanshan (Sam) Ma – FEMS Microbiology Ecology

Impact of Initial Feeding and Molting on Tachypleus tridentatus Gut Microbiota – Fengze Miao et al.,Current Microbiology 

Osmotic stress induces gut microbiota community shift in fish – Keng Po Lai et al.,Environmental Microbiology

The Gut-Eye Axis: Lessons Learned from Murine Models – Jason L. Floyd & Maria B. Grant – Ophthalmology and Therapy 

The colonic mucosa-associated microbiome in SIV infection: shift towards Bacteroidetes coincides with mucosal CD4+ T cell depletion and enterocyte damage – Kristina Allers et al., Scientific Reports  

Plant or Soil Microbiomes

Re-Analysis of 16S Amplicon Sequencing Data Reveals Soil Microbial Population Shifts in Rice Fields under Drought Condition – Seok-Won Jang et al,Rice 

Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations – Ryan S. McClure et al., Scientific Reports 

Potential microbial bioindicators of phosphorus mining in a temperate deciduous forest – Laura M. Mason et al.,Journal of Applied Microbiology

Phylogenetic signals and predictability in plant-soil feedbacks – Elizabeth M. Wandrag et al.,New Phytologist

Genomics / Bioinformatics

The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites – Feifei Xu et al.,Microbial Genomics 

LEMMI: A continuous benchmarking platform for metagenomics classifiers – Mathieu Seppey et al.,Genome Research

Other papers

Preprint: Metagenome-assembled genomes from Monte Cristo Cave (Diamantina, Brazil) reveal prokaryotic lineages as functional models for life on Mars – Amanda G Bendia et al., BioRxiv 

Preprint: Exploring metal resistance genes and mechanisms in copper enriched metal ore metagenome – Esmaeil Forouzan Sr. et al., BioRxiv

SARS-CoV-2 Preprints

Preprint: Alpha-1 antitrypsin inhibits SARS-CoV-2 infection – Lukas Wettstein et al.,BioRxiv

June 7, 2020

Have a nice Sunday! Today, in this brief Digest, we have few papers about Microbiome and Health, including studies on Fibromyalgia, ALS and Hepatitis E infection. Additionally, we have papers about SARS-CoV-2. Stay safe!  

Microbiome research

Review: Microbiome in Health and Disease – Edward M Giles – Journal of Paediatrics and Child Health

Metabolic Syndrome, Depression, and Fibromyalgia Syndrome Prevalence in Patients With Irritable Bowel Syndrome: A Case-Control Study – Muharrem Bayrak – Medicine

Preprint: Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity – Nicholas D Youngblut – bioRxiv

Amyotrophic Lateral Sclerosis and Intestinal Microbiota-Toward Establishing Cause and Effect – Marc Gotkine – Gut Microbes

Freeze-dried Fecal Samples Are Biologically Active After Long-Lasting Storage and Suited to Fecal Microbiota Transplantation in a Preclinical Murine Model of Clostridioides difficile Infection – Julie Reygner – Gut Microbes

Altered Fecal Microbiota on the Expression of Th Cells Responses in the Exacerbation of Patients With Hepatitis E Infection – Jian Wu – Journal of Viral Hepatitis

Covid-19 papers

Preprint: An OpenData portal to share COVID-19 drug repurposing data in real time – Kyle R. Brimacombe – bioRxiv

Preprint: Comparative study of four SARS-CoV-2 Nucleic Acid Amplification Test (NAAT) platforms demonstrates that ID NOW performance is impaired substantially by patient and specimen type – Paul Robert Lephart – bioRxiv

A Systematic Review of Neurological Manifestations of SARS-CoV-2 Infection: The Devil Is Hidden in the Details – Michele Romoli – European Journal of Neurology

Concomitant Brain Arterial and Venous Thrombosis in a COVID-19 Patient – Maria Malentacchi – European Journal of Neurology

February 28, 2020

Good morning/afternoon y’all! today’s digest features some interesting-to-read genral biotech and ecology papers, as weel as the first gene catalouge of the vaginal microbiome, American pets microbiome revealed, cool microbiome engineering for biocontrol purpose in agriculture, a bunch of salt- and sweet-water microbiome studies and more!

Have a great weekend! put the guilt aside and enjoy some time with your spouse, family, pets, hobbies and anything else that you enjoy!

General Science

is is a very cool paper, beuatifuly presenting the connection and applicatino of two very ‘hot’ topics in today biotechnology world- AI and drug discovery:A Deep Learning Approach to Antibiotic Discovery- A Deep Learning Approach to Antibiotic Discovery, Jonathan M. Stokes, Cell

** Novel Outlook in Microbial Ecology: Nonmutualistic Interspecies Electron Transfer, Roman Moscoviz, Trends in Microbiology

A solution to minimum sample size for regressions, David J. Jenkins , PLOS One

The relationship between the host genome, microbiome, and host phenotype, Harald Brussow, Env. Micro.

Human microbiome

** A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina, Bing Ma, Nature Communications

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention, Jessica A. Grembi, Sci. Rep.

Analysis of healthy reference ranges for clinically relevant gut microbial indicators: A large web-based cohort study in Japan, Satoshi Watanabe , bioRxiv

Short chain fatty acids produced by colonizing intestinal commensal bacterial interaction with expressed breast milk are anti-inflammatory in human immature enterocytes, Nan Zheng, PLOS One

Animal microbiome

Characterization of gut microbiomes of household pets in the United States using a direct-to-consumer approach, Aashish R. Jha, PLOS One

Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome, Samuel J. Bowers, PLOS One

Insect microbiome

**Engineering bacterial symbionts of nematodes improves biocontrol potential of the western corn rootworm, Ricardo A. R. Machado, Nature Biotechnology

Plant and soil microbiome

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome, Siwen Deng , bioRxiv

Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes, Yuting Liang , Env. Micro.

Network analysis infers the wilt pathogen invasion associated with non-detrimental bacteria, Qiolong Hu , npj biofims and microbiomes

Marine microbiome

Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings, Marcela Franca Dias, Water Research

Niche partitioning of methane-oxidizing bacteria along the oxygen–methane counter gradient of stratified lakes, Magdalena J. Mayr, ISME

A metagenomic assessment of microbial eukaryotic diversity in the global ocean, Aleix Obiol, Mol. Eco. Res.

Ocean acidification affects microbial community and invertebrate settlement on biofilms, Katie S. Nelson, Sci. Rep.

Understanding and creating biocementing beachrocks via biostimulation of indigenous microbial communities, Asha A. Ramachandran , Env. Biotech.

February 8, 2020

Have a nice Saturday, everyone! Today, in this Digest: several reviews, including some of them about the microbiome and Irritable Bowel Syndrome, Autism, Chemotherapy, C. difficile infection and more. Additionally, there is a very interesting study (Obata et al., Nature), showing new evidence about the relationship between the microbiota, the gut, and the nervous system. 

 

Human and General Microbiome

Neuronal programming by microbiota regulates intestinal physiology – Yuuki Obata – Nature

Fecal metatranscriptomics and glycomics suggest that bovine milk oligosaccharides are fully utilized by healthy adults – Samuel T. Westreich – The Journal of Nutritional Biochemistry

Review: Microbiome and Its Role in Irritable Bowel Syndrome – Mark Pimentel – Digestive Diseases and Sciences 

Review: Gut microbiota changes in children with autism spectrum disorder: a systematic review – Lucius Kang Hua Ho – Gut Pathogens

Review: Relationship Between the Gut Microbiome and Systemic Chemotherapy – Samantha M. Ervin – Digestive Diseases and Sciences 

Review: The infant gut microbiome as a microbial organ influencing host well-being – Francesca Turroni – Italian Journal of Pediatrics

Review: Increasing incidence of inflammatory bowel disease in children and adolescents: the significance of the environmental factors – Sowon Park – CEP

Review: Insights into the Role of Human Gut Microbiota in Clostridioides difficile Infection – Melina Kachrimanidou – Microorganisms (MDPI)

Review: Role of Dietary Nutrients in the Modulation of Gut Microbiota: A Narrative Review – Qi Yang – Nutrients

Opinion: Food, microbes, sex and old age: on the plasticity of gastrointestinal innervation – Tomotsune Ameku – Current Opinion in Neurobiology

The effects of proton pump inhibitors on the microbiome in young children – EI Levy – Acta Paedriatica

Targeted Approaches for In Situ Gut Microbiome Manipulation – Gail A. M. Cresci – JPEN

Dysbiosis of the Oral Ecosystem in Severe Congenital Neutropenia Patients – Egija Zaura – Proteomics Clinical Applications

Comparing Analytical Methods for the Gut Microbiome and Aging: Gut Microbial Communities and Body Weight in the Osteoporotic Fractures in Men (MrOS) Study – Michelle Shardell – The Journals of Gerontology: Series A

Oral and Gut Microbial Diversity and Immune Regulation in Patients with HIV on Antiretroviral Therapy – Medini K. Annavajhala – mSphere

Characteristics and Dysbiosis of the Gut Microbiome in Renal Transplant Recipients – J. Casper Swarte – Journal of Clinical Medicine

Comparison of serum microbiome composition in bipolar and major depressive disorders – Sang Jin Rhee – Journal of Psychiatric Research

 

Animal Microbiome / Animal Experiments

Review: Ruminal microbiome and microbial metabolome: effects of diet and ruminant host – C. J. Newbold – Animal

Review: Comparative methane production in mammalian herbivores – M. Clauss – Animal

Review: Regulation of gastrointestinal and renal transport of calcium and phosphorus in ruminants – M. R. Wilkens – Animal

Degeneration of the intestinal microbial community in PI3Kγ-knockout mice – Yi Li – Microbial Pathogenesis

Toxicity, gut microbiota and metabolome effects after copper exposure during early life in SD rats – Juan Dai – Toxicology

Evaluation of the effects of anthelmintic administration on the fecal microbiome of healthy dogs with and without subclinical Giardia spp. and Cryptosporidium canis infections – Madeline A. Fujishiro – PLoS ONE

Time of Feeding Alters Obesity-Associated Parameters and Gut Bacterial Communities, but Not Fungal Populations, in C57BL/6 Male Mice – Marie van der Merwe – CDN

Moderation effects of food intake on the relationship between urinary microbiota and urinary interleukin-8 in female type 2 diabetic patients – Fengping Liu – PeerJ

 

Beneficial Microbes and Compounds

Review: Surface components and metabolites of probiotics for regulation of intestinal epithelial barrier – Qing Liu – Microbial Cell Factories 

Polysaccharides from Polygonatum kingianum improve glucose and lipid metabolism in rats fed a high fat diet – Wen Gu – Biomedicine & Pharmacotherapy

Structural modulation of gut microbiota during alleviation of non-alcoholic fatty liver disease with Gynostemma pentaphyllum in rats – Shu-Hua Shen – BMC Complementary Medicine and Therapies

 

Plant Microbiome

Metagenomics methods for the study of plant-associated microbial communities: A review – Ayomide Emmanuel Fadiji – Journal of Microbiological Methods

Duckweed hosts a taxonomically similar bacterial assemblage as the terrestrial leaf microbiome – Kenneth Acosta – PLoS ONE

 

Bioinformatics

Computational Modeling of the Human Microbiome – Shomeek Chowdhury – Microorganisms (MDPI)

Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling – Valery V. Panyukov – International Journal of Molecular Sciences

February 2, 2020

Have a nice Sunday! Today, in this Digest we have several papers about the relationship between the microbiome and different neurological/psychological conditions, such as ASD, depression or anxiety, or about the microbiome and the inflammatory bowel disease. Enjoy!

 

Human and General Microbiome

Review: Host-microbiota interactions in inflammatory bowel disease – Roberta Caruso – Nature Reviews Immunology 

Review: Considering gut microbiota in treatment of type 2 diabetes mellitus – Aneseh Adeshirlarijaney – Gut Microbes

Review: Gut Dysbiosis Dysregulates Central and Systemic Homeostasis via Suboptimal Mitochondrial Function: Assessment, Treatment and Classification Implications – George Anderson – Current Topics in Medicinal Chemistry

Book Chapter: Immune-Kynurenine Pathways and the Gut Microbiota-Brain Axis in Anxiety Disorders – Alper Evrensel – Anxiety Disorders 

Book Chapter: Autism and Gut-Brain Axis: Role of Probiotics – Saravana Babu Chidambaram – Personalized Food Intervention and Therapy for Autism Spectrum Disorder Management

Review: Microbial-Based and Microbial-Targeted Therapies for Inflammatory Bowel Diseases – Akihiko Oka – Digestive Diseases and Sciences

Precision Microbiome Modulation with Discrete Dietary Fiber Structures Directs Short-Chain Fatty Acid Production – Edward C. Deehan – Cell Host and Microbe

Urinary microbiome in uncomplicated and interstitial cystitis: is there any similarity? – Süleyman Yıldırım – World Journal of Urology

The gut microbiota response to helminth infection depends on host sex and genotype – Fei Ling – The ISME Journal 

Metabolism of multiple glycosaminoglycans by Bacteroides thetaiotaomicron is orchestrated by a versatile core genetic locus – Didier Ndeh – Nature Communications

Gestational diabetes and the human salivary microbiota: a longitudinal study during pregnancy and postpartum – Mie K. W. Crusell – BMC Pregnancy and Childbirth 

Vaginal dysbiosis associated-bacteria Megasphaera elsdenii and Prevotella timonensis induce immune activation via dendritic cells – Nienke H.van Teijlingen – Journal of Reproductive Immunology

Variability in Skin Microbiota between Smokers, Former Smokers, and Non-Smokers – Katherine G. Thompson – Journal of the American Academy of Dermatology

Microbiota changes and Intestinal Microbiota Transplantation in Liver Diseases and Cirrhosis – Jasmohan S. Bajaj – Journal of Hepatology

Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin – Wei Zhou – Cell

 

Animal Microbiome and Animal Experiments

Effect of probiotic administration on gut microbiota and depressive behaviors in mice – Quan Feng Liu – DARU Journal of Pharmaceutical Sciences

Deciphering the bifidobacterial population within the canine and feline gut microbiota – Giulia Alessandri – Applied and Environmental Microbiology

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system – Yaron Krotman – Microbiome

Prenatal exposure to glufosinate ammonium disturbs gut microbiome and induces behavioral abnormalities in mice – Tianyu Dong – Journal of Hazardous Materials

High prevalence of Phasi Charoen-like virus from wild-caught Aedes aegypti in Grenada, W.I. as revealed by metagenomic analysis – Maria E. Ramos-Nino – PLoS ONE

Common structuring principles of the Drosophila melanogaster microbiome on a continental scale and between host and substrate – Yun Wang – Environmental Microbiology Reports

Community assembly of the native C. elegans microbiome is influenced by time, substrate, and individual bacterial taxa – Julia Johnke – Environmental Microbiology 

 

Environmental Microbiome

Patterns of local, intercontinental and inter-seasonal variation of soil bacterial and eukaryotic microbial communities – Johan De Gruyter – FEMS Microbiology Ecology

Dynamics and ecological distributions of the Archaea microbiome from inland saline lakes (Monegros Desert, Spain) – Mateu Menéndez-Serra – FEMS Microbiology Ecology

 

January 24, 2020

Have a nice weekend! Today in this Digest, we have several papers about different interventions, microbes, and compounds with positive properties. And, of course, more papers. Enjoy.

 

Human and General Microbiome

Review: The microbiota and the hypothalamus-pituitary-adrenocortical (HPA) axis, implications for anxiety and stress disorders – Linoy Mia Frankiensztajn – Current Opinion in Neurobiology

Review: The Role of Meat Protein in Generation of Oxidative Stress and Pathophysiology of Metabolic Syndromes – Muhammad Ijaz Ahmad – Food Science of Animal Resources

Identifying determinants of bacterial fitness in a model of human gut microbial succession – Lihui Feng – PNAS

Reduced environmental bacterial load during early development and gut colonisation has detrimental health consequences in Japanese quail. – Ngare Wilkinson  – Heliyon

Review: Immunological Role of the Maternal Uterine Microbiome in Pregnancy: Pregnancies Pathologies and Alterated Microbiota – Jonah Bardos – Frontiers in Immunology

Association between the faecal short-chain fatty acid propionate and infant sleep – Anne-Louise M. Heath – European Journal of Clinical Nutrition

Prenatal dietary supplements influence the infant airway microbiota in a randomized factorial clinical trial – Mathis H. Hjelmsø – Nature Communications 

Physical fitness in community-dwelling older adults is linked to dietary intake, gut microbiota, and metabolomic signatures – Josué L. Castro‐Mejía – Aging Cell

Temporal Gut Microbial Changes Predict Recurrent Clostridiodes Difficile Infection in Patients With and Without Ulcerative Colitis – Allen A Lee – Inflammatory Bowel Diseases

Impacts of the Plateau Environment on the Gut Microbiota and Blood Clinical Indexes in Han and Tibetan Individuals – Zhilong Jia – mSystems

Intestinal microbes influence development of thymic lymphocytes in early life – Maria Ennamorati – PNAS

The cervicovaginal mucus barrier to HIV-1 is diminished in bacterial vaginosis – Thuy Hoang – PLoS Pathogens

Establishing high-accuracy biomarkers for colorectal cancer by comparing fecal microbiomes in patients with healthy families – Jian Yang – Beneficial Microbes

Characteristic gut microbiota and predicted metabolic functions in women with PCOS – Ling Zhou – Endocrine Connections 

Obese adolescents with PCOS have altered biodiversity and relative abundance in gastrointestinal microbiota – Beza Jobira – The Journal of Clinical Endocrinology & Metabolism

Association between blood omega-3 polyunsaturated fatty acids and the gut microbiota among breast cancer survivors – A. Horigome – Beneficial Microbes

Editorial: Processed food affects the gut microbiota: The revolution has started – Michael A Kamm – Journal of Gastroenterology and Hepatology

Commentary: mSphere of Influence: the Mycobiota in Human Health and Disease – Soo Chan Lee – mSphere

 

Animal Microbiota and Animal Model experiments

Letter: TCF-1 deficiency influences the composition of intestinal microbiota and enhances susceptibility to colonic inflammation – Guotao Yu – Protein & Cell 

Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota – Rieka Chijiiwa – Microbiome

Antidepressant treatment with fluoxetine during pregnancy and lactation modulates the gut microbiome and metabolome in a rat model relevant to depression – Anouschka S Ramsteijn – Gut Microbes

 

Beneficial Microbes and Compounds

Review: Fecal microbiota transplantation in disease therapy – Hanna Antushevich – Clinica Chimica Acta

Review: Microbiota and alcohol use disorder: are psychobiotics a novel therapeutic strategy? – Alicia Rodriguez-Gonzalez – Current Pharmaceutical Design

Mining possible associations of faecal A. muciniphila colonisation patterns with host adiposity and cardiometabolic markers in an adult population – E.K. Mitsou – Beneficial Microbes

Probiotics maintain intestinal secretory immunoglobulin A levels in healthy formula-fed infants: a randomised, double-blind, placebo-controlled study – L. Xiao – Beneficial Microbes

Effect of rice bran fermented with Saccharomyces cerevisiae and Lactobacillus plantarum on gut microbiome of mice fed high-sucrose diet – J. Shibayama – Beneficial Microbes

Inulin with different degrees of polymerization protects against diet-induced endotoxemia and inflammation in association with gut microbiota regulation in mice – Li-Li Li – Scientific Reports

Understanding the Scope of Do-It-Yourself Fecal Microbiota Transplant – Chiazotam Ekekezie – The American Journal of Gastroenterology

Milk Fermented by Lactobacillus paracasei NCC 2461 (ST11) Modulates the Immune Response and Microbiota to Exert its Protective Effects Against Salmonella typhimurium Infection in Mice – Leonardo Borges Acurcio – Probiotics and Antimicrobial Proteins 

Recovery of Lactobacillus casei strain Shirota (LcS) from faeces of healthy Singapore adults after intake of fermented milk – W.W.T. Khine – Beneficial Microbes

Seabuckthorn (Hippophaë rhamnoides) Freeze-Dried Powder Protects against High-Fat Diet-Induced Obesity, Lipid Metabolism Disorders by Modulating the Gut Microbiota of Mice – Caixia Guo – Nutrients

Chitooligosaccharides Modulate Glucose-Lipid Metabolism by Suppressing SMYD3 Pathways and Regulating Gut Microflora – Qiutong Wang – Marine Drugs

Lactobacillus and Pediococcus ameliorate progression of non-alcoholic fatty liver disease through modulation of the gut microbiome – Na Young Lee – Gut Microbes

Review: Antimicrobials for food and feed; a bacteriocin perspective – Paula M O’Connor – Current Opinion in Biotechnology

 

Bioinformatics

Transfer index, NetUniFrac and some useful shortest path-based distances for community analysis in sequence similarity networks – Henry Xing – Bioinformatics

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota – Christian Diener – mSystems

January 20, 2020

Have a nice monday! Today, in this Digest we have a good amount of papers about different beneficial interventions based on the microbiome such as probiotics, synbiotics and others. We have also papers about the microbiome in brain disorders, new evidence about microbiota changes in IBS, the impact of early antibiotic use on infant microbiota and the relation between mycobiome and childhood caries. Enjoy!

Human and General Microbiome

Review: The Reproductive Microbiome: An Emerging Driver of Sexual Selection, Sexual Conflict, Mating Systems, and Reproductive Isolation – Melissah Rowe – Trends in Ecology and Evolution

Systematic Review: Gut microbial changes of patients with psychotic and affective disorders: A systematic review – Nina Vindegaard – Schizophrenia Research

Review: The progress of gut microbiome research related to brain disorders – Sibo Zhu – Journal of Neuroinflammation

Review: Unraveling How Candida albicans Forms Sexual Biofilms – Austin M. Perry – Journal of Fungi

In Brief: Host-microbiome interactions lost during flight – Ashley York – Nature Reviews Microbiology

Evidence of altered mucosa-associated and fecal microbiota composition in patients with Irritable Bowel Syndrome – Johanna Sundin – Scientific Reports

Antibiotics in early life associate with specific gut microbiota signatures in a prospective longitudinal infant cohort – Katri Korpela – Pediatric Research 

Activated Drp1-mediated mitochondrial ROS influence the gut microbiome and intestinal barrier after hemorrhagic shock – Chenyang Duan – Aging

Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages – Aurélie Mathieu – Nature Communications

Impact of commonly used drugs on the composition and metabolic function of the gut microbiota – Arnau Vich Vila – Nature Communications

Site-specific profiling of the dental mycobiome reveals strong taxonomic shifts during progression of early childhood caries – Lauren M. O’Connell – Applied and Environmental Microbiology

Influence of gastrectomy for gastric cancer treatment on faecal microbiome and metabolome profiles – Pande Putu Erawijantari – Gut (BMJ)

Dysbiosis Signatures of Fecal Microbiota in South African Infants with Respiratory, Gastrointestinal, and Other Diseases – Srinivasan Krishnamoorthy – The Journal of Pediatrics

Cervicovaginal Microbiome and Urine Metabolome Paired Analysis Reveals Niche Partitioning of the Microbiota in Patients with Human Papilloma Virus Infections – Nataliya Chorna – Metabolites (MDPI)

Animal Microbiomes and Animal Model Experiments

The mitochondrial negative regulator MCJ modulates the interplay between microbiota and the host during ulcerative colitis – Miguel Angel Pascual-Itoiz – Scientific Reports

Effects of peptidoglycan on the development of steatohepatitis – Meiling Jin – Biochimica et Biophysica Acta (BBA) – Molecular and Cell Biology of Lipids

Phylosymbiosis across deeply diverging lineages in omnivorous cockroaches – Kara A. Tinker – Applied and Environmental Microbiology

Metagenomic shotgun analyses reveal complex patterns of intra- and interspecific variation in the intestinal microbiomes of codfishes – Even Sannes Riiser – Applied and Environmental Microbiology

Beneficial Microbes and Compounds

Review: Effects of probiotics on type II diabetes mellitus: a meta-analysis – Yun-Wen Tao – Journal of Translational Medicine

Opinion: Improving Risk-Benefit in Faecal Transplantation through Microbiome Screening – Lito E. Papanicolas – Trends in Microbiology

Akkermansia muciniphila Prevents Fatty Liver, Decreases Serum Triglycerides, and Maintains Gut Homeostasis – Sejeong Kim – Applied and Environmental Microbiology

Lactobacillus Protects Against S. Typhimurium-Induced Intestinal Inflammation by Determining the Fate of Epithelial Proliferation and Differentiation – Xiaoxi Lu – Molecular Nutrition & Food Research

Probiotics Prevent Dysbiosis and the Raise in Blood Pressure in Genetic Hypertension: Role of Short-chain Fatty Acids – Iñaki Robles‐Vera – Molecular Nutrition & Food Research

Tuna Bone Powder Alleviates Glucocorticoid-Induced Osteoporosis Via Coregulation of the NF-κB and Wnt/β-Catenin Signaling Pathways and Modulation of Gut Microbiota Composition and Metabolism – Chenyang Lu – Molecular Nutrition & Food Research

A 2-strain mixture of Lactobacillus acidophilus in the treatment of irritable bowel syndrome: A placebo-controlled randomized clinical trial – Stéphane Sadrin – Digestive and Liver Disease

Lactobacillus reuteri DSM 17938 and Magnesium Oxide in Children with Functional Chronic Constipation: A Double-Blind and Randomized Clinical Trial – Megumi Kubota – Nutrients

Chemical Profile, Antioxidative, and Gut Microbiota Modulatory Properties of Ganpu Tea: A Derivative of Pu-erh Tea – Yuying Zheng – Nutrients

Effects of Synbiotic Supplement on Human Gut Microbiota, Body Composition and Weight Loss in Obesity – Igor N. Sergeev – Nutrients

Antidiabetic Effect of Casein Glycomacropeptide Hydrolysates on High-Fat Diet and STZ-Induced Diabetic Mice via Regulating Insulin Signaling in Skeletal Muscle and Modulating Gut Microbiota – Qichen Yuan – Nutrients

December 31, 2019

This is the last Microbiome Digest post from 2019! As part of the MD team, I want to say: Thank you very much for follow this blog. Have a great 2020, better than the 2019. The best for you! 

Cheers as well to Dr. Elies Bik (the MD founder) and all the other member of the MD team. -JPC

 

Human and General Microbiome

Review: Microbiota impacts on chronic inflammation and metabolic syndrome – related cognitive dysfunction – María Arnoriaga-Rodríguez – Reviews in Endocrine and Metabolic Disorders

Review: A Review of the Brain-Gut-Microbiome Axis and the Potential Role of Microbiota in Alzheimer’s Disease –  Sun, Miao – Journal of Alzheimer’s Disease

Meta-Analysis: The lacking effects of prebiotic products on decreasing adiposity parameters in overweight and obese individuals: a systematic review and meta-analysis – Hua Qu – Current Medicinal Chemistry

Review: Autoimmune Hepatitis-Immunologically Triggered Liver Pathogenesis-Diagnostic and Therapeutic Strategies – Elisabeth Suche – Journal of Immunology Research

Review: A Comprehensive Review and Update on the Pathogenesis of Inflammatory Bowel Disease – Qingdong Guan – Journal of Immunology Research

Review: Advances in Gut Microbiota of Viral Hepatitis Cirrhosis – Yixuan Wang – BioMed Research International

Review: Mechanisms of gastrointestinal microflora on drug metabolism in clinical practice – Chaonan Sun – Saudi Pharmaceutical Journal

Review: Gut microbiome and response to checkpoint inhibitors in non-small cell lung cancer-A review – Misako Nagasaka – Critical Reviews in Oncology/Hematology

Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi – Siddhika Pareek – npj Biofilms and Microbiomes 

Faecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection: Experience with Lyophilized Oral Capsules – E. Reigadas – Journal of Hospital Infection

Vaginal microbiome diversity and preterm birth: results of a nested case-control study in Peru – Freida Blostein – Annals of Epidemiology

Disordered cutaneous microbiota in systemic lupus erythematosus – Cancan Huang – Journal of Autoimmunity

Transfer of skin microbiota between two dissimilar autologous microenvironments: A pilot study – Benji Perin  – PLoS ONE

 

Animal Microbiome

Alleviating chronic kidney disease progression through modulating the critical genus of gut microbiota in a cisplatin-induced Lanyu pig model – Ya-Jane Lee – Journal of Food and Drug Analysis

Microbiota changes in a pediatric acute lymphocytic leukemia mouse model – Yajing Song – MicrobiologyOpen

Impact of chronic exposure to trichlorfon on intestinal barrier, oxidative stress, inflammatory response and intestinal microbiome in common carp (Cyprinus carpio L.) – Xulu Changa – Environmental Pollution

Glucocorticoid and dietary effects on mucosal microbiota in canine inflammatory bowel disease – Todd Atherly – PLoS ONE

Effect of endometriosis on the fecal bacteriota composition of mice during the acute phase of lesion formation – Josefine Hantschel – PLoS ONE

Involvement of the gut microbiota and barrier function in glucocorticoid induced osteoporosis – Jonathan D Schepper – ASBMR

 

Food Microbiome

Exploring functional core bacteria in fermentation of a traditional Chinese food, Aspergillus-type douchi – Huilin Yang – PLoS ONE

High Throughput Sequencing Technologies as a New Toolbox for Deep Analysis, Characterization and Potentially Authentication of Protection Designation of Origin Cheeses? – Elena Kamilari – International Journal of Food Science 

 

Beneficial Microbes and Compounds

Blueberry Attenuates Liver Fibrosis, Protects Intestinal Epithelial Barrier, and Maintains Gut Microbiota Homeostasis – Zhiqiang Yan – Canadian Journal of Gastroenterology and Hepatology

Cortex Phellodendri extract’s anti-diarrhea effect in mice related to its modification of gut microbiota – Baoyang Xu – Biomedicine & Pharmacotherapy

 

Environmental and Water Microbiome

Tossed ‘good luck’ coins as vectors for anthropogenic pollution into aquatic environment – Alejandro Martínez – Environmental Pollution

Single molecule sequencing reveals response of manganese-oxidizing microbiome to different biofilter media in drinking water systems – Xin Zhao – Water Research

Enterococci Isolated from Trout in the Bukovec Water Reservoir and Čierny Váh River in Slovakia and Their Safety Aspect – Andrea Lauková – BioMed Research International

 

Bioinformatics / Databases

Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species – Serena Manara – Genome Biology

Sufficient dimension reduction for compositional data – Diego Tomassi – Biostatistics

Cultivated Escherichia coli diversity in intestinal microbiota of Crohn’s disease patients and healthy individuals: Whole genome data – Maria Siniagina – Data in Brief

 

December 29, 2019

Have a nice sunday!  Today we have papers about the microbiome in martial arts athletes, more research about Fusobacterium and colorectal cancer, the effect of light in atopic dermatitis and the effect of alcohol binge in a mouse model, among other papers.  

Human and General Microbiome

Review: The Gut-Liver-Kidney axis: novel regulator of fatty liver associated chronic kidney disease – Desh Raj – Pharmacological Research

Characteristics of the gut microbiota in professional martial arts athletes: A comparison between different competition levels – Ru Liang – PLoS One

The balance between breast cancer and the immune system: challenges for prognosis and clinical benefit from immunotherapies – Constantin N. Baxevanis – Seminars in Cancer Biology

Review: Host- and Microbiota-Derived Extracellular Vesicles, Immune Function, and Disease Development – Laurence Macia – International Journal of Molecular Sciences

Recent advances in understanding the natural history of the otitis media microbiome and its response to environmental pressures – Robyn L. Marsh – International Journal of Pediatric Otorhinolaryngology

Association of autophagy status with amount of Fusobacterium nucleatum in colorectal cancer – Koichiro Haruki – The Journal of Pathology

Effects of 308 nm excimer light treatment on the skin microbiome of atopic dermatitis patients – Yuko Kurosaki – Photodermatology, Photoimmunology and Photomedicine

Rapid Multiplex Real-Time PCR Method for the Detection and Quantification of Selected Cariogenic and Periodontal Bacteria – Jan Lochman – Diagnostics

Review: Biomarkers of a Healthy Nordic Diet-From Dietary Exposure Biomarkers to Microbiota Signatures in the Metabolome – Rikard Landberg – Nutrients

 

Animal Microbiome

Gut microbiota of provisioned and wild rhesus macaques (Macaca mulatta) living in a limestone forest in southwest Guangxi, China – Ting Chen – MicrobiologyOpen

The Diversity of the Endobiotic Bacterial Communities in the Four Jellyfish Species – Qing Liu – Polish Journal of Microbiology

Switching to a Healthy Diet Prevents the Detrimental Effects of Western Diet in a Colitis-Associated Colorectal Cancer Model – Charlotte Gröschel – Nutrients

The Effect of Thermal Stress on the Bacterial Microbiome of Exaiptasia diaphana – Leon M. Hartman – Microorganisms

Pretreatment with Yeast-Derived Complex Dietary Polysaccharides Suppresses Gut Inflammation, Alters the Microbiota Composition, and Increases Immune Regulatory Short-Chain Fatty Acid Production in C57BL/6 Mice – Radhika Gudi – The Journal of Nutrition

Long-lasting microbial dysbiosis and altered enteric neurotransmitters in adult rats following adolescent binge ethanol exposure – Ryan P. Vetreno – Addiction Biology

 

Beneficial Microbes and Compounds

Minireview: Use of Synbiotics for Ulcerative Colitis Treatment – Marianna Roselli –  Current Clinical Pharmacology

The Structure Features and Improving Effects of Polysaccharide from Astragalus membranaceus on Antibiotic-Associated Diarrhea – Shanshan Ll – Antibiotics

Deep-Fried Atractylodis Rhizoma Protects against Spleen Deficiency-Induced Diarrhea through Regulating Intestinal Inflammatory Response and Gut Microbiota – Kun Shi – International Journal of Molecular Sciences

Hafnia alvei HA4597 Strain Reduces Food Intake and Body Weight Gain and Improves Body Composition, Glucose, and Lipid Metabolism in a Mouse Model of Hyperphagic Obesity – Nicolas Lucas – Microorganisms

 

Wastewater Microbiome

Microbiome changes and oxidative capability of an anaerobic PCB dechlorinating enrichment culture after oxygen exposure – Bruna Matturro – New Biotechnology

 

Plant Microbiome

Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota – Bruna Matturro – Microorganisms

Metagenome sequencing of fingermillet-associated microbial consortia provides insights into structural and functional diversity of endophytes – M. K. Prasannakumari – 3 Biotech 

Resilience to multiple stressors in an aquatic plant and its microbiome – Anna M. O’Brien – American Journal of Botany

 

Techniques

Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics – Yiming Huang – Nucleic Acids Research