July 5, 2020

Pregnancy and early life
Natural environments in the urban context and gut microbiota in infants – Neilsen et al. – Environment International

Human nearly-sterile sites
Breast cancer colonization by Fusobacterium nucleatum accelerates tumor growth and metastatic progression – Parhi et al. – Nature Communications

Enrichment of the airway microbiome in people living with HIV with potential pathogenic bacteria despite antiretroviral therapy – Rofael et al. – EClinicalMedicine

Human microbiome in vitro and ex vivo experiments
Triclosan has a robust, yet reversible impact on human gut microbial composition in vitro – Mahalak et al. – PLOS One

Animal experiments
Alterations of gut microbiota and serum bile acids are associated with parenteral nutrition-associated liver disease – Wang et al. – Journal of Pediatric Surgery

Colonic microbiome profiles for improved feed efficiency can be identified despite major effects of farm of origin and contemporary group in pigs – Vigors et al. – Animal

Gut microbiota profiles of commercial laying hens infected with tumorigenic viruses – Wan et al. – BMC Veterinary Research

Alterations of gut microbiota contribute to the progression of unruptured intracranial aneurysms – Li et al. – Nature Communications

Animal microbiome
Review: The Effects of Nutrition on the Gastrointestinal Microbiome of Cats and Dogs: Impact on Health and Disease – Wernimont et al. – Frontiers in Microbiology

Individual and Site-Specific Variation in a Biogeographical Profile of the Coyote Gastrointestinal Microbiota – Sugden et al. – Microbial Ecology

Assessment of bacterial diversity of Rhipicephalus microplus ticks from two livestock agroecosystems in Antioquia, Colombia – Segura et al. – PLOS One

Microbiome diversity in Diaphorina citri populations from Kenya and Tanzania shows links to China – Ajene et al. – PLOS One

Plant, root, and soil microbiome
Metagenomics analysis of fungal communities associated with postharvest diseases in pear fruits under the effect of management practices – Zambounis et al. – Archives of Microbiology

Water and extremophile microbiome
The Efficacy of Hydrogen Peroxide in Mitigating Cyanobacterial Blooms and Altering Microbial Communities across Four Lakes in NY, USA – Lusty and Gobler – Toxins

Seasonal effects of river flow on microbial community coalescence and diversity in a riverine network – Luo et al. – FEMS Microbiology Ecology

Microbial community composition across a coastal hydrological system affected by submarine groundwater discharge (SGD) – Adyasari et al. – PLOS One

The contribution of microbial communities in polymetallic nodulesto the diversity of the deep-sea microbiome of the Peru Basin(4130–4198 m depth) – Molari et al. – Biogeosciences

Probiotics / prebiotics
Review: Toward a systematic design of smart probiotics – Choudhary and Mahadevan – Current Opinion in Biotechnology

A Novel Non-Digestible, Carrot-Derived Polysaccharide (cRG-I) Selectively Modulates the Human Gut Microbiota while Promoting Gut Barrier Integrity: An Integrated In Vitro Approach – Van den Abbeele et al. – Nutrients

Bioinformatics
Review: What Is Metagenomics Teaching Us, and What Is Missed? – New and Brito – Annual Review of Microbiology

June 25, 2020

COVID19
Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography – Kneller et al. – Nature Communications

Pregnancy and early life
Review – Maternal and infant factors that shape neonatal gut colonisation by bacteria – O’Neill et al. – Expert Review of Gastroenterology & Hepatology

Perinatal risk factors for fecal antibiotic resistance gene patterns in pregnant women and their infants – Sosa-Moreno et al. – PLOS One

Human gut microbiome
Microbial and metabolomic profiles in correlation with depression and anxiety co-morbidities in diarrhoea-predominant IBS patients – Liu et al. – BMC Microbiology

Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study – Tahseen et al. – Scientific Reports

Animal experiments
Effects of Drinking Water Temperature and Flow Rate during Cold Season on Growth Performance, Nutrient Digestibility and Cecum Microflora of Weaned Piglets – Zhang et al. – Animals

Effects of supplementary feeding on the rumen morphology and bacterial diversity in lambs – Lv et al. – PeerJ

Evaluating the association between feed efficiency and the fecal microbiota of early-life Duroc pigs using 16S rRNA sequencing – Si et al. – AMB Express

Establishment and Stability of the Murine Oral Microbiome – Ramos et al. – Journal of Dental Research

Effects of chronic treatment with new strains of Lactobacillus plantarum on cognitive, anxiety- and depressive-like behaviors in male mice – Barros-Santos et al. – PLOS One

Animal microbiome
Reproductive hormones mediate changes in the gut microbiome during pregnancy and lactation in Phayre’s leaf monkeys – Mallott et al. – Scientific Reports

Plant, root, and soil microbiome
Microbial community types and signature-like soil bacterial patterns from fortified prehistoric hills of Thuringia (Germany) – Kohler et al. – Community Ecology

Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality – Zhou et al. – Nature Communications

Prairie plants harbor distinct and beneficial root-endophytic bacterial communities – Adu-Oppong et al. – PLOS One

Water and extremophile microbiome
Surviving marginalized reefs: assessing the implications of the microbiome on coral physiology and survivorship – Roitman et al. – Coral Reefs

Microbial Communities Associated with Farmed Genypterus chilensis: Detection in Water Prior to Bacterial Outbreaks Using Culturing and High-Throughput Sequencing – Levican et al. – Animals

Energy-Efficient Single-Stage Nitrite Shunt Denitrification with Saline Sewage through Concise Dissolved Oxygen (DO) Supply: Process Performance and Microbial Communities – Zhuang et al. – Microorganisms

Food microbiology
Dynamics of Microbial Communities, Texture and Flavor in Suan zuo yu during Fermentation – Wang et al. – Food Chemistry

Probiotics / prebiotics
Bifidobacterium bifidum Suppresses Gut Inflammation Caused by Repeated Antibiotic Disturbance Without Recovering Gut Microbiome Diversity in Mice – Ojima et al. – Frontiers in Microbiology

Bacillus subtilis PB6 based probiotic supplementation plays a role in the recovery after the necrotic enteritis challenge – Aljumaah et al. – PLOS One

Bioinformatics
BiomMiner: An advanced exploratory microbiome analysis and visualization pipeline – Shamsaddini et al. – PLOS One

May 3, 2020

COVID19
Preprint: Lack of Reinfection in Rhesus Macaques Infected with SARS-CoV-2 – Bao – Biorxiv

Events and jobs

Call for papers: BMC Health Policy and the Management of Antimicrobial Resistance in LMICs

Pregnancy and early life

Hospital Regimens Including Probiotics Guide the Individual Development of the Gut Microbiome of Very Low Birth Weight Infants in the First Two Weeks of Life – Kurath-Koller – Nutrients

Maternal H. pylori is associated with differential fecal microbiota in infants born by vaginal delivery – Hernandez – Scientific Reports


Human gut microbiome

Review: The link between autism spectrum disorder and gut microbiota: A scoping review – Nitschke – Autism


Intestinal Dysbiosis in Carriers of Carbapenem-Resistant Enterobacteriaceae – Korach-Rechtman – mSphere

Human oral microbiome
Review: Oral microbiome: possible harbinger for children’s health – Xiao – International Journal of Oral Science

Animal experiments

Komagataeibacter hansenii CGMCC 3917 Alleviates Alcohol-Induced Liver Injury by Regulating Fatty Acid Metabolism and Intestinal Microbiota Diversity in Mice – Lin – Royal Society of Chemistry


Putting the microbiota to work: Epigenetic effects of early life antibiotic treatment are associated with immune-related pathways and reduced epithelial necrosis following Salmonella Typhimurium challenge in vitro – Costa – PlosOne


Combined Prebiotic and Microbial Intervention Improves Oral Cholera Vaccination Responses in a Mouse Model of Childhood Undernutrition – Di Luccia – Cell Host & Microbe

Animal microbiome

Establishment and Stability of the Murine Oral Microbiome – Abusleme – Journal of Dental Research

Effect of stocking density and effective fiber on the ruminal bacterial communities in lactating Holstein cows – Clemmons – PeerJ

Plant, root, and soil microbiome

Long-term continuously monocropped peanut significantly changed the abundance and composition of soil bacterial communities – Chen – PeerJ


Compared to conventional, ecological intensive management promotes beneficial proteolytic soil microbial communities for agro-ecosystem functioning under climate change-induced rain regimes – Lori – Scientific Reports


Organic mulching positively regulates the soil microbial communities and ecosystem functions in tea plantation – Zhang – BMC Microbiology

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

Aequorivita sinensis sp. nov., isolated from sediment of the East China Sea, and reclassification of Vitellibacter todarodis as Aequorivita todarodis comb. nov. and Vitellibacter aquimaris as Aequorivita aquimaris comb. nov. – Wang – Microbiology Society


Bioprospecting and characterization of pigmented halophilic archaeal strains from Algerian hypersaline environments with analysis of carotenoids produced by Halorubrum sp. BS2 – Sahli – Journal of Basic Microbiology


Effects of a deep-sea mining experiment on seafloor microbial communities and functions after 26 years – Vonnahme – Science Advances

Food microbiology

Review: Traditionally fermented pickles: How the microbial diversity associated with their nutritional and health benefits? – Behera – Journal of Functional Foods

Bioinformatics

Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control – Bichat – Frontiers in Microbiology


Techniques
Preprint: Freshwater monitoring by nanopore sequencing – Urban – Biorxiv

March 30, 2020

Please stay home and help flatten the curve! Continuing the past few days, the first papers will be COVID-19 related

COVID-19
Preprint: SARS-CoV-2 specific antibody responses in COVID-19 patients Okba et al.

Anti–spike IgG causes severe acute lung injury by skewing macrophage responses during acute SARS-CoV infection Liu et al.

Human Vaginal Microbiome
Study Protocol: Protocol for a Longitudinal Analysis of the Vaginal Microbiome from a Pregnant Cohort of African Women in Nigeria Odogwu et al.

Human Gut Microbiome
Ruminococcus gnavus bacteremia, an uncommon presentation of a common member of the human gut microbiota: case report and literature review Lefever et al.

Water Microbiome
Preprint: Dissecting the toxicity and mitigating the impact of harmful Prymnesium blooms in the UK waters of the Norfolk Broads Wagstaff et al.

Techniques
Preprint: Internal control for process monitoring of clinical metagenomic next-generation sequencing of urine samples Janes et al.

Microbes in the News
Study explores the beneficial effects of healthy dietary patterns on gut microbiome mental_daily