In today’s digest it was quite hard to pick just few papers, since there are many, many interesting papers. From mentioned reviews I would recommend the one by H. Bokhari on the exploitation of microbial forensics and nanotechnology for the monitoring of emerging pathogens and the one by J. R. Bober on engineering probiotics and microbes for biomedical applications. From other papers I would like to highlight the one by M. Mehrshad and enigmatic SAR202 cluster, the one by A. C. Lehours and biogeographic patterns of aerobic anoxygenic phototrophic bacteria and the one by E. M. Llufrio and how fluorescence activated cell sorting introduces oxidative stress and alters the metabolic state of cells. Don’t forget to check on news, where you can read about metagenomic clustering powered by supercomputers, while in general science section there is an interesting article by B. Barros on ‘scientific knowledge percolation process’ or how scientific information diffuse into the social sphere.
General microbiome
Review: Exploitation of microbial forensics and nanotechnology for the monitoring of emerging pathogens – Habib Bokhari – Critical Reviews in Microbiology
The aryl hydrocarbon receptor as a moderator of host-microbiota communication – Limin Zhang – Current Opinion in Toxicology
Pregnancy and early life
The Role of the Microbiome in the Developmental Origins of Health and Disease – Leah T. Stiemsma – Pediatrics
Human gut microbiome
Translocation of a gut pathobiont drives autoimmunity in mice and humans – S. Manfredo Vieira – Science
Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome – Laura-Isobel McCall – PLOS One
How to Increase the Butyrate-Producing Capacity of the Gut Microbiome: Do IBD Patients Really Need Butyrate Replacement and Butyrogenic Therapy? – Stanislav Sitkin – Journal of Crohn’s and Colitis
Effect of Faecal Microbiota Transplantation for Treatment of Clostridium difficile Infection in Patients with Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis of Cohort Studies – Tuo chen – Journal of Crohn’s and Colitis
Animal experiments
Supplementation of Bacillus subtilis based probiotic reduces heat stress-related behaviors and inflammatory response in broiler chickens – W C Wang – Journal of Animal Science
Comparisons of bacterial and Archaeal Communities in the Rumen and a Dual-Flow Continuous Culture Fermentation System using Amplicon Sequencing – I J Salfer – Journal of Animal Science
The Microbiome Regulates Pulmonary Responses to Ozone in Mice – Youngji Cho – American Journal of Respiratory Cell and Molecular Biology
Bifidobacteria exert species-specific effects on constipation in BALB/c mice – Linlin Wang – Food & Function
Animal microbiome
Comparative Analysis of the Gut Bacterial Community of Four Anastrepha Fruit Flies (Diptera: Tephritidae) Based on Pyrosequencing – Carmen Ventura – Current Microbiology
Metagenomic insights into lignocellulose-degrading genes through Illumina-based de novo sequencing of the microbiome in Vietnamese native goats’ rumen – Thi Huyen Do – The Journal of General and Applied Microbiology
Plant, root, and soil microbiome
Colonization of Eggplant by Endophytic Bacteria Antagonistic to Ralstonia solanacearum, the Bacterial Wilt Pathogen – Gauri A. Achari – Proceedings of the National Academy of Sciences, India Section B: Biological Sciences
Landscape scale factors affecting prevalence of Escherichia coli in surface soil include land cover type, edge interactions, and soil pH – Nicholas Dusek – Applied and Environmental Microbiology
Nigericin and grisorixin methyl ester from the Algerian soil-living Streptomyces youssoufiensis SF10 strain: a computational study on their epimeric structures and evaluation of glioblastoma stem cells growth inhibition – Nassima Leulmi – Natural Product Research
Interacting effect of diclofop-methyl on the rice rhizosphere microbiome and denitrification – Haifeng Qian – Pesticide Biochemistry and Physiology
Indigenous Pseudomonas spp. Strains from the Olive (Olea europaea L.) Rhizosphere as Effective Biocontrol Agents against Verticillium dahliae: From the Host Roots to the Bacterial Genomes – Carmen Gómez-Lama Cabanás – Frontiers in Microbiology
Resveratrol as a growth substrate for bacteria from the rhizosphere – Zohre Kurt – Applied and Environmental Microbiology
Predicting the structure of soil communities from plant community taxonomy, phylogeny, and traits – Jonathan W. Leff – The ISME Journal
Diversity of microbial communities potentially involved in mercury methylation in rice paddies surrounding typical mercury mining areas in China – Xin Liu – Microbiology Open
Bacterial Preferences for Specific Soil Particle Size Fractions Revealed by Community Analyses – Michael Hemkemeyer – Frontiers in Microbiology
Volatile compounds from beneficial or pathogenic bacteria differentially regulate root exudation, transcription of iron transporters, and defense signaling pathways in Sorghum bicolor – Erasto Hernández-Calderón – Plant Molecular Biology
The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader’s niche – C. A. Mallon – The ISME Journal
Soil contamination alters the willow root and rhizosphere metatranscriptome and the root–rhizosphere interactome – Etienne Yergeau – The ISME Journal
Bioaugmentation of chlorothalonil-contaminated soil with hydrolytically or reductively dehalogenating strain and its effect on soil microbial community – Xi-Hui Xu – Journal of Hazardous Materials
Water and extremophile microbiome
Biogeographic patterns of aerobic anoxygenic phototrophic bacteria reveal an ecological consistency of phylogenetic clades in different oceanic biomes – Anne-Catherine Lehours – Scientific Report
Mercury-methylating bacteria are associated with zooplankton: a proof-of-principle survey in the Baltic Sea – Elena Gorokhova – bioRxiv
Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community – Laura Gómez-Consarnau – bioRxiv
Effects of nutrient loading on sediment bacterial and pathogen communities within seagrass meadows – Songlin Liu – Microbiology Open
Chapter 17 – Rhizosphere Metabolite Profiling: An Opportunity to Understand Plant-Microbe Interactions for Crop Improvement -Amit Verma – Crop Improvement Through Microbial Biotechnology
Chapter 22 – Plant-Microbe Interaction and Genome Sequencing: An Evolutionary Insight – Krishna K. Sharma – Crop Improvement Through Microbial Biotechnology
Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain) – Blanca Vera-Gargallo – Genes
Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management – Domenico Savio – Wiley Interdisciplinary Reviews: Water
Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus, and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments – Kathleen M. Scott – Environmental Microbiology
Data Article: Bioinformatics delimitation based on sequence data of the psychrophilic and psychrotolerant actinobacteria isolated from the Polar Frontal waters of the Antarctic Ocean – Palaniappan Sivasankar – Data in Brief
Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity – Kai Tang – Frontiers in Microbiology
The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling – Maliheh Mehrshad – The ISME Journal
The widespread dissemination of integrons throughout bacterial communities in a riverine system – Gregory C. A. Amos – The ISME Journal
Expression profiling of host and virus during a coccolithophore bloom provides insights into the role of viral infection in promoting carbon export – Uri Sheyn – The ISME Journal
Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations – Sarahi L. Garcia – The ISME Journal
Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota – Lin-Xing Chen – The ISME Journal
Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases – Andrea G. Bravo – The ISME Journal
Diazotroph diversity and nitrogen fixation in the coral Stylophora pistillata from the Great Barrier Reef – Michael P. Lesser – The ISME Journal
Multiple colonist pools shape fiddler crab-associated bacterial communities – Catalina Cuellar-Gempeler – The ISME Journal
Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp. – Mikhail A. Moldovan – Frontiers in Microbiology
Halotolerant Exiguobacterium profundum PHM11 Tolerate Salinity by Accumulating L-Proline and Fine-Tuning Gene Expression Profiles of Related Metabolic Pathways – Vikas K. Patel – Frontiers in Microbiology
The predictability of a lake phytoplankton community, over time-scales of hours to years – Mridul K. Thomas – Ecology Letters
Built environment
Anaerobic Ammonium-Oxidizing Bacteria in Cow Manure Composting – Tingting Wang – Journal of Microbiology and Biotechnology
Petrophilic, Fe(III) Reducing Exoelectrogen Citrobacter sp. KVM11, Isolated From Hydrocarbon Fed Microbial Electrochemical Remediation Systems – Krishnaveni Venkidusamy – Frontiers in Microbiology
Inhibitors degradation and microbial response during continuous anaerobic conversion of hydrothermal liquefaction wastewater – Buchun Sia – Science of The Total Environment
Food microbiology
Different temperatures select distinctive acetic acid bacteria species and promotes organic acids production during Kombucha tea fermentation – Francesca De Filippis – Food Microbiology
Staphylococcus aureus undergoes major transcriptional reorganization during growth with Enterococcus faecalis in milk – Gabriela NogueiraViçosa – Food Microbiology
Variability within the dominant microbiota of sliced cooked poultry products at expiration date in the Belgian retail – Wim Geeraerts – Food Microbiology
Changes in microbial communities and quality attributes of white muscle and dark muscle from common carp (Cyprinus carpio) during chilled and freeze-chilled storage – Qian Li – Food Microbiology
Microbial diversity and chemical analysis of the starters used in traditional Chinese sweet rice wine – Haiying Cai – Food Microbiology
Structure of association networks in food bacterial communities – Eugenio Parente – Food Microbiology
Shifts in spinach microbial communities after chlorine washing and storage at compliant and abusive temperatures – Ganyu Gu – Food Microbiology
Probiotics / prebiotics
Effective identification of Lactobacillus casei group species: genome-based selection of the gene mutL as the target of a novel multiplex PCR assay – Benedetta Bottari – Microbiology
Phages and viruses
A Holistic Assessment of the Risks and Benefits of the Synthesis of Horsepox Virus – Diane Di Euliis – mSphere
Biotechnology
Impact of anti-acidification microbial consortium on carbohydrate metabolism of key microbes during food waste composting – Caihong Song – Bioresource Technology
Review: Synthetic Biology Approaches to Engineer Probiotics and Members of the Human Microbiota for Biomedical Applications – Josef R. Bober – Annual Review of Biomedical Engineering
Techniques
Sorting Cells Alters Their Redox State and Cellular Metabolome – Elizabeth M. Llufrio – Redox Biology
Microbes in the news
Ibuprofen Counters Key Bacteria in Lungs of CF Patients, Study Shows
Bacteria in your intestines can trigger autoimmune diseases
A game changer: Metagenomic clustering powered by supercomputers
Science, publishing, and career
Scientific knowledge percolation process and social impact: a case study on the biotechnology and microbiology perceptions on Twitter – Beatriz Barros – Science and Public Policy