Zegarra-Ruiz DF, El Beidaq A, Iñiguez AJ, Lubrano Di Ricco M, Manfredo Vieira S, Ruff WE, Mubiru D, Fine RL, Sterpka J, Greiling TM, Dehner C, Kriegel MA. Cell Host Microbe. 01 2019.
COMMENT: This paper is focused in the analysis of the influence of gut microbiome in autoimmunity, specifically in the Systemic Lupus Erythematosus (SLE) pathogenesis and evolution. As in many other pathologies related with gut-microbiome, the impairment... + info
Competition in Biofilms between Cystic Fibrosis Isolates of Pseudomonas aeruginosa Is Shaped by R-Pyocins.
Oluyombo O, Penfold CN, Diggle SP. MBio. Jan 2019.
COMMENT: A major clinical problem in individuals with cystic fibrosis (CF) is the chronic infection of the lungs caused by Pseudomonas aeruginosa. In this interesting paper the authors study the role that the S- and R-pyocins play in the competition... + info
Lee KH, Gordon A, Shedden K, Kuan G, Ng S, Balmaseda A, Foxman B. PLoS One. 2019. doi: 10.1371/journal.pone.0207898.
COMMENT: Study on the relation of the nose/throat microbiome and the susceptibility of influenza virus infection + info
Kerfahi D, Tripathi BM, Dong K, Kim M, Kim H, Ferry Slik JW, Go R, Adams JM. Microb Ecol. Jan 2019. doi: 10.1007/s00248-018-1215-z.
COMMENT: In this work soil metagenomes from Arctic regions are compared with those from Equatorial tropics. The results in some cases confirm the predictions of the authors but in others cases are unexpected and to understand why the actual features... + info
The antimicrobial resistome in relation to antimicrobial use and biosecurity in pig farming, a metagenome-wide association study in nine European countries.
Van Gompel L, Luiken REC, Sarrazin S, Munk P, Knudsen BE, Hansen RB, Bossers A, Aarestrup FM, Dewulf J, Wagenaar JA, Mevius DJ, Schmitt H, Heederik DJJ, Dorado-García A, Smit LAM. J Antimicrob Chemother. Jan 2019. doi: 10.1093/jac/dky518.
COMMENT: Antimicrobial resistance is a global public health problem. It is known that veterinary antimicrobial use (AMU) promotes antimicrobial resistance (AMR) in animals, and AMR can be transmitted from animals to humans. The resistome is the term... + info
Minority species influences microbiota formation: the role of Bifidobacterium with extracellular glycosidases in bifidus flora formation in breastfed infant guts.
Gotoh A, Ojima MN, Katayama T. Microb Biotechnol. Jan 2019. doi: 10.1111/1751-7915.13366.
COMMENT: The article highlights the importance of rare Bifidobacterium longum strains with extracellular glycosidases as keystone species in the formation of the bifidus flora in breastfed infants. + info
Characterization of novel lignocellulose-degrading enzymes from the porcupine microbiome using synthetic metagenomics.
Thornbury M, Sicheri J, Slaine P, Getz LJ, Finlayson-Trick E, Cook J, Guinard C, Boudreau N, Jakeman D, Rohde J, McCormick C. PLoS One. 2019. doi: 10.1371/journal.pone.0209221.
COMMENT: This work combines metagenomics and synthetic biology strategies to obtain new enzymes with lignocellulose-degrading capacity. First, a shotgun metagenomics using de novo assembly approach from porcupine fecal DNA samples allowed the selection... + info
Singh I, Kuscuoglu M, Harkins DM, Sutton G, Fouts DE, Nelson KE. BMC Bioinformatics. Jan 2019. doi: 10.1186/s12859-018-2580-9.
COMMENT: Ometa is a data-driven web application designed for the management and tracking of contextual metadata (specimen, spatial-temporal, phenotypic characteristics) that facilitate the organization, administration, curation, sharing and consulting... + info
Docherty KM, Gutknecht JLM. Ecol Appl. Jan 2019. doi: 10.1002/eap.1858.
COMMENT: Soil microbial restoration practices are used to produce climate-ready ecosystems, a major challenge faced by land managers, farmers and restoration scientists. Little is known about whether addition of whole communities including... + info
Antibiotic treatment triggers gut dysbiosis and modulates metabolism in a chicken model of gastro-intestinal infection.
Le Roy CI, Woodward MJ, Ellis RJ, La Ragione RM, Claus SP. BMC Vet Res. Jan 2019. doi: 10.1186/s12917-018-1761-0.
COMMENT: Antibiotic use is associated with a reduction of gut microbiota diversity. This study uses an interesting chicken infection model to understand host systemic metabolic and gut microbiota response to colonization of the digestive tract by... + info
The Microbiome Stress Project: Toward a Global Meta-Analysis of Environmental Stressors and Their Effects on Microbial Communities.
Rocca JD, Simonin M, Blaszczak JR, Ernakovich JG, Gibbons SM, Midani FS, Washburne AD. Front Microbiol. 2018. doi: 10.3389/fmicb.2018.03272.
COMMENT: The Microbiome Stress Project is an open-access database of environmental and host-associated 16S rRNA amplicon sequencing studies, that will facilitate cross-study analyses of microbiome responses to natural and anthropogenic stressors.... + info
Townsend GE, Han W, Schwalm ND, Raghavan V, Barry NA, Goodman AL, Groisman EA. Proc Natl Acad Sci U S A. Jan 2019. doi: 10.1073/pnas.1813780115.
COMMENT: This work is focused on how fructose and sucrose impact the colonization of the gut microbiome by Bacteroides thetaiotaomicron, a commensal bacteria abundant in healthy gut human microbiomes. Surprisingly the authors find, based on experiments... + info
Wright AT. Nat Microbiol. Jan 2019. doi: 10.1038/s41564-018-0325-1.
COMMENT: This article, within the section News and Views, comments the work of Chittim, L. C., Martinez del Campo, A. & Balskus E. P. in Nat Microbiol. 2019 Jan;4(1):155-163, about gut bacterial phospholipase D and its involvement in... + info
Streptococcus macedonicus strains isolated from traditional fermented milks: resistance to gastrointestinal environment and adhesion ability.
Khaldi TEM, Kebouchi M, Soligot C, Gomri MA, Kharroub K, Le Roux Y, Roux E. Appl Microbiol Biotechnol. Jan 2019. doi: 10.1007/s00253-019-09651-z.
COMMENT: Bacterial strains must meet certain selection criteria to be qualified as probiotic. Probiotic bacteria must have an ecological origin, survival capability to low pH and to bile salts stress and a good adhesion ability to epithelial cells. In... + info
Mechanisms Underlying Microbial-Mediated Changes in Social Behavior in Mouse Models of Autism Spectrum Disorder.
Sgritta M, Dooling SW, Buffington SA, Momin EN, Francis MB, Britton RA, Costa-Mattioli M. Neuron. Jan 2019.
COMMENT: This interesting article analyzes the capacity of Lactobacillus reuteri for reversing social deficits in Mouse Models of ASD (Autism Spectrum Disorder). The work shows that, surprisingly, the treatment with L. reuteri is able to rescue the... + info
Exploiting the Oral Microbiome to Prevent Tooth Decay: Has Evolution Already Provided the Best Tools?
Baker JL, Edlund A. Front Microbiol. 2018. doi: 10.3389/fmicb.2018.03323.
COMMENT: This minireview describes therapeutic strategies for caries prevention and treatment that exploit the protective effects of the healthy oral flora to prevent dental caries. + info
Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features.
Alessandri G, Milani C, Mancabelli L, Mangifesta M, Lugli GA, Viappiani A, Duranti S, Turroni F, Ossiprandi MC, van Sinderen D, Ventura M. Environ Microbiol. Jan 2019. doi: 10.1111/1462-2920.14540.
COMMENT: The authors investigate the canine gut microbiota analyzing a large number of canine fecal samples from healthy dogs belonging to 51 different breeds. + info
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.
Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, Beghini F, Manghi P, Tett A, Ghensi P, Collado MC, Rice BL, DuLong C, Morgan XC, Golden CD, Quince C, Huttenhower C, Segata N. Cell. Jan 2019.
COMMENT: This article describes a lot of work done analyzing 9,428 human metagenomic samples and trying to reconstruct the microbial genomes that there were in each sample using de novo assembly and binning procedures. The results of this work... + info
The effects of afforestation on soil bacterial communities in temperate grassland are modulated by soil chemical properties.
Wu SH, Huang BH, Gao J, Wang S, Liao PC. PeerJ. 2019. doi: 10.7717/peerj.6147.
COMMENT: After grassland afforestation, abiotic, biotic and ecological function changes occur in the soil ecosystem what might break the stasis of soil physicochemical properties and the dynamic balance of microbiota. + info
Fusobacterium nucleatum promotes chemoresistance to 5-fluorouracil by upregulation of BIRC3 expression in colorectal cancer.
Zhang S, Yang Y, Weng W, Guo B, Cai G, Ma Y, Cai S. J Exp Clin Cancer Res. 01 2019. doi: 10.1186/s13046-018-0985-y.
COMMENT: The authors investigate the potential role of Fusobacterium nucleatum present in the gut in the resistance of colorectal cancers to 5-fluoracil #cancer #gutmicrobiome #microbiome + info
Li W, Deng Y, Chu Q, Zhang P. Cancer Lett. Jan 2019.
COMMENT: The authors discuss the relationships between the gut microbiome, the host immune system and cancer immunotherapy. The article summarizes what it is known about the role of the human microbiome in the development of certain kinds of cancers.... + info
Dill-McFarland KA, Tang ZZ, Kemis JH, Kerby RL, Chen G, Palloni A, Sorenson T, Rey FE, Herd P. Sci Rep. Jan 2019. doi: 10.1038/s41598-018-37298-9.
COMMENT: Diet, gender and high blood sugar have been correlated with different gut microbiota profiles.. However, there is not much information about how social relationships could impact in both, microbiota and health. Based on the results... + info
Escherichia coli promotes DSS‑induced murine colitis recovery through activation of the TLR4/NF‑κB signaling pathway.
Lu J, Dong B, Chen A, He F, Peng B, Wu Z, Cao J, Li W. Mol Med Rep. Jan 2019. doi: 10.3892/mmr.2019.9848.
COMMENT: Intestinal microbiome is critical in inflammatory bowel disease (IBD). This study investigated the effects of Escherichia coli in the dextran sulfate sodium (DSS)‑induced colitis mouse model of IBD. The... + info
Lamoureux C, Guilloux CA, Beauruelle C, Jolivet-Gougeon A, Héry-Arnaud G. Crit Rev Microbiol. Jan 2019. doi: 10.1080/1040841X.2018.1549019.
COMMENT: This review is centered on the study of anaerobes in Cystic Fibrosis (CF) and tries to solve the role of them in CF pathophysiology using the information about the metabolites that anaerobes produce (metabolome) and about the anaerobe... + info
Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth.
Jiao S, Chen W, Wei G. Appl Environ Microbiol. Jan 2019.
COMMENT: This work investigates the soil microbial communities response to chemical contamination studying the long-term changes in soil ecosystems. 16S analysis for taxonomic profiling and shotgun metagenomics approaches for functional profiling... + info
Fecal microbiota transplantation for treatment of recurrent C. difficile infection: An updated randomized controlled trial meta-analysis.
Hui W, Li T, Liu W, Zhou C, Gao F. PLoS One. 2019. doi: 10.1371/journal.pone.0210016.
COMMENT: In this article the authors reviewed recent articles about controlled clinical trials using fecal microbiota transplantation (FMT) for treatment of Clostridioides difficile (formerly called Clostridium difficile) recurrent... + info
Ellegaard KM, Engel P. Nat Commun. 01 2019. doi: 10.1038/s41467-019-08303-0.
COMMENT: The study is focused on assessing the diversity of the honey bee gut microbiota, for that they have studied the gut microbiota of 54 bees in three age groups (young, middle-aged, and old) sampled from two adjacent colonies (one of which was... + info
Tanoue T, Morita S, Plichta DR, Skelly AN, Suda W, Sugiura Y, Narushima S, Vlamakis H, Motoo I, Sugita K, Shiota A, Takeshita K, Yasuma-Mitobe K, Riethmacher D, Kaisho T, Norman JM, Mucida D, Suematsu M, Yaguchi T, Bucci V, Inoue T, Kawakami Y, Olle B, Roberts B, Hattori M, Xavier RJ, Atarashi K, Honda K. Nature. Jan 2019. doi: 10.1038/s41586-019-0878-z.
COMMENT: The authors identify a consortium of 11 bacterial strains capable of inducing IFN-gamma producing CD8 T cells at the intestine. Results in mice show that the consortium enhanced resistance to Listeria monocytogenes and efficacy of immunotherapy... + info
Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads.
Liu J, Lian Q, Chen Y, Qi J. Nucleic Acids Res. Jan 2019. doi: 10.1093/nar/gkz017.
COMMENT: This article presents a new assembler called MetaPA for metagenomic and metatranscriptomic sequences that is focused on knowing the set of proteins that there are in each sample. Unlike other assembly methods based in nucleotide sequences,... + info
Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin.
He Z, Gharaibeh RZ, Newsome RC, Pope JL, Dougherty MW, Tomkovich S, Pons B, Mirey G, Vignard J, Hendrixson DR, Jobin C. Gut. 02 2019. doi: 10.1136/gutjnl-2018-317200.
COMMENT: The study reveals the effect of Campylobacter jejuni on the development of colorectal cancer in mouse models + info
Tongue coating microbiome data distinguish patients with pancreatic head cancer from healthy controls
Haifeng Lu, Zhigang Ren, Ang Li, Jinyou Li, Shaoyan Xu, Hua Zhang, Jianwen Jiang, Jiezuan Yang, Qixia Luo, Kai Zhou, Shusen Zheng & Lanjuan Li. Journal of Oral Microbiology, 11:1, Jan 2019. DOI: 10.1080/20002297.2018.1563409.
COMMENT: The study reveals differences in the tongue coating microbiome in patients with Pancreatic head carcinoma comparing with Liver cancer patients and healthy controls. + info
Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut.
Jiang X, Hall AB, Arthur TD, Plichta DR, Covington CT, Poyet M, Crothers J, Moses PL, Tolonen AC, Vlamakis H, Alm EJ, Xavier RJ. Science. Jan 2019. doi: 10.1126/science.aau5238.
COMMENT: This article is centered around the study of inversion-mediated phase variation. In this inversion events a DNA sequence is inverted, resulting in an ON to OFF switch or vice versa resulting in the expression or not of the gene/genes located... + info
Pedron R, Esposito A, Bianconi I, Pasolli E, Tett A, Asnicar F, Cristofolini M, Segata N, Jousson O. Microbiome. Jan 2019. doi: 10.1186/s40168-019-0625-6.
Comment: A comprehensive study of a spring water microbiome, the taxonomic composition was inferred by 16S amplicon sequencing, shotgun metagenomics, high-throughput culturing and Metagenome-assembled genomes (MAGs). + info
Tap J, Cools-Portier S, Pavan S, Druesne A, Öhman L, Törnblom H, Simren M, Derrien M. Sci Rep. Jan 2019. doi: 10.1038/s41598-018-36953-5.
COMMENT: 16S rRNA gene sequencing of fecal samples is an effective and non-invasive method to study the gut microbiome. An appropiate storage of sample material is essential to avoid the introduction of bias in microbial community composition.... + info
Influenza-induced immune suppression to methicillin-resistant Staphylococcus aureus is mediated by TLR9.
Martínez-Colón GJ, Warheit-Niemi H, Gurczynski SJ, Taylor QM, Wilke CA, Podsiad AB, Crespo J, Bhan U, Moore BB. PLoS Pathog. Jan 2019. doi: 10.1371/journal.ppat.1007560.
COMMENT: This article describes one important finding that could be involved in the known fact that methicillin-resistant Staphylococcus aureus (MRSA) lung infections have increased mortality if they appeared after influenza infection. ... + info
Armstrong H, Alipour M, Valcheva R, Bording-Jorgensen M, Jovel J, Zaidi D, Shah P, Lou Y, Ebeling C, Mason AL, Lafleur D, Jerasi J, Wong GK, Madsen K, Carroll MW, Huynh HQ, Dieleman LA, Wine E. Microbiome. Jan 2019. doi: 10.1186/s40168-018-0604-3.
Comment: Inflammatory bowel diseases (IBD) that include Crohn disease (CD) and ulcerative colitis (UC) display a reduced microbial diversity and elevated IgG levels in the lumen. Previous studies suggest that coating of intestinal bacteria with IgA... + info
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease.
Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Daníelsdóttir AD, Krecke M, Merten D, Haraldsdóttir HS, Heinken A, Heirendt L, Magnúsdóttir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Žagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I. Nucleic Acids Res. Jan 2019. doi: 10.1093/nar/gky992.
COMMENT: A new database with knowledge data about human metabolism within five interlinked resources 'Human metabolism', 'Gut microbiome', 'Disease', 'Nutrition', and 'ReconMaps' available at: www... + info
gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data.
Shi W, Qi H, Sun Q, Fan G, Liu S, Wang J, Zhu B, Liu H, Zhao F, Wang X, Hu X, Li W, Liu J, Tian Y, Wu L, Ma J. Nucleic Acids Res. Jan 2019. doi: 10.1093/nar/gky1008.
COMMENT: A new database for metagenomics called The Global Catalogue of Metagenomics (gcMeta) appears in the Nucleic Acids Research Database issue of 2019. gcMeta includes data of samples from human and environmental microbiomes freely... + info
Comparison of the Gut Microbiota of Centenarians in Longevity Villages of South Korea with Those of Other Age Groups.
Kim BS, Choi CW, Shin H, Jin SP, Bae JS, Han M, Seo EY, Chun J, Chung JH. J Microbiol Biotechnol. Jan 2019. doi: 10.4014/jmb.1811.11023.
COMMENT: Several studies have observed connections between gut microbiota and longevity, however discrepancies have been observed due to differences in diet, life style, genetic factors, and analyses methods. In this study, the authors analyze the... + info
Huh H, Wong S, St Jean J, Slavcev R. Adv Drug Deliv Rev. Jan 2019.
COMMENT: This review discuss the bacteriophage interaction with the human body and their ability to penetrate various human tissues such as gut, brain, skin, circulatory and respiratory system, and its current applications in phage therapy. + info
Harrison OJ, Linehan JL, Shih HY, Bouladoux N, Han SJ, Smelkinson M, Sen SK, Byrd AL, Enamorado M, Yao C, Tamoutounour S, Van Laethem F, Hurabielle C, Collins N, Paun A, Salcedo R, O'Shea JJ, Belkaid Y. Science. Jan 2019.
COMMENT: Because of the extraordinary number of antigens expressed by the microbiota, a significant fraction of skin-resident T cells are expected to be commensal-specific, accumulating over time in response to successive exposure to new commensals.... + info
Peeters T, Penders J, Smeekens SP, Galazzo G, Houben B, Netea MG, Savelkoul PH, Gyssens IC. Future Microbiol. Jan 2019. doi: 10.2217/fmb-2018-0203.
COMMENT + info
Old Instillations and New Implications in Bladder Cancer: The Urinary Microbiome and Intravesical BCG.
Bajic P, Wolfe AJ, Gupta GN. BJU Int. Jan 2019. doi: 10.1111/bju.14683.
COMMENT + info