Everard A, Belzer C, Geurts L, Ouwerkerk JP, Druart C, Bindels LB, Guiot Y, Derrien M, Muccioli GG, Delzenne NM, et al. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. P Natl Acad Sci USA. 2013;110(22):9066–71.
Article
CAS
Google Scholar
Bleau C, Karelis AD, St-Pierre DH, Lamontagne L. Crosstalk between intestinal microbiota, adipose tissue and skeletal muscle as an early event in systemic low-grade inflammation and the development of obesity and diabetes. Diabetes Metab Res Rev. 2015;31(6):545–61.
Article
CAS
Google Scholar
Sabatino A, Regolisti G, Cosola C, Gesualdo L, Fiaccadori E. Intestinal microbiota in type 2 diabetes and chronic kidney disease. Curr Diab Rep. 2017;17(3):16.
Article
Google Scholar
Wu T, Trahair LG, Little TJ, Bound MJ, Zhang X, Wu H, Sun Z, Horowitz M, Rayner CK, Jones KL. Effects of Vildagliptin and metformin on blood pressure and heart rate responses to small intestinal glucose in type 2 diabetes. Diabetes Care. 2017;40(5):702–5.
Article
CAS
Google Scholar
Gyang VP, Chuang TW, Liao CW, Lee YL, Akinwale OP, Orok A, Ajibaye O, Babasola AJ, Cheng PC, Chou CM, et al. Intestinal parasitic infections: current status and associated risk factors among school aged children in an archetypal African urban slum in Nigeria. J Microbiol Immunol Infect. 2019;52(1): 106–113.
Article
Google Scholar
Marcial-Coba MS, Marshall IPG, Schreiber L, Nielsen DS. High-Quality Draft Genome Sequence of Lactobacillus casei Strain Z11, Isolated from a Human Adult Intestinal Biopsy Sample. Genome Announc. 2017;5(28):e00634–17.
Volynets V, Kuper MA, Strahl S, Maier IB, Spruss A, Wagnerberger S, Konigsrainer A, Bischoff SC, Bergheim I. Nutrition, intestinal permeability, and blood ethanol levels are altered in patients with nonalcoholic fatty liver disease (NAFLD). Dig Dis Sci. 2012;57(7):1932–41.
Article
CAS
Google Scholar
Kelly P. Nutrition, intestinal defence and the microbiome. Proc Nutr Soc. 2010;69(2):261–8.
Article
Google Scholar
Che C, Pang X, Hua X, Zhang B, Shen J, Zhu J, Wei H, Sun L, Chen P, Cui L, et al. Effects of human fecal flora on intestinal morphology and mucosal immunity in human flora-associated piglet. Scand J Immunol. 2009;69(3):223–33.
Article
CAS
Google Scholar
Sesto N, Koutero M, Cossart P. Bacterial and cellular RNAs at work during Listeria infection. Future Microbiol. 2014;9(9):1025–37.
Article
CAS
Google Scholar
Fernandes PC, Dolinger EJ, Abdallah VO, Resende DS, Gontijo Filho PP, Brito D. Late onset sepsis and intestinal bacterial colonization in very low birth weight infants receiving long-term parenteral nutrition. Rev Soc Bras Med Trop. 2011;44(4):447–50.
Article
Google Scholar
Levine A. Exclusive enteral nutrition: clues to the pathogenesis of Crohn's disease. Nestle Nutr Inst Workshop Ser. 2014;79:131–40.
Article
Google Scholar
Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W, Pettersson S. Host-gut microbiota metabolic interactions. Science. 2012;336(6086):1262–7.
Article
CAS
Google Scholar
Rastall RA, Gibson GR. Recent developments in prebiotics to selectively impact beneficial microbes and promote intestinal health. Curr Opin Biotechnol. 2015;32:42–6.
Article
CAS
Google Scholar
Li Y, Poroyko V, Yan Z, Pan L, Feng Y, Zhao P, Xie Z, Hong L. Characterization of intestinal microbiomes of Hirschsprung's disease patients with or without Enterocolitis using Illumina-MiSeq high-throughput sequencing. PLoS One. 2016;11(9):e0162079.
Article
Google Scholar
Moreau MM, Eades SC, Reinemeyer CR, Fugaro MN, Onishi JC. Illumina sequencing of the V4 hypervariable region 16S rRNA gene reveals extensive changes in bacterial communities in the cecum following carbohydrate oral infusion and development of early-stage acute laminitis in the horse. Vet Microbiol. 2014;168(2–4):436–41.
Article
CAS
Google Scholar
Barbosa A, Reiss A, Jackson B, Warren K, Paparini A, Gillespie G, Stokeld D, Irwin P, Ryan U. Prevalence, genetic diversity and potential clinical impact of blood-borne and enteric protozoan parasites in native mammals from northern Australia. Vet Parasitol. 2017;238:94–105.
Article
Google Scholar
Barrios C, Beaumont M, Pallister T, Villar J, Goodrich JK, Clark A, Pascual J, Ley RE, Spector TD, Bell JT, et al. Gut-microbiota-metabolite Axis in early renal function decline. PLoS One. 2015;10(8):e0134311.
Article
Google Scholar
Momose Y, Maruyama A, Iwasaki T, Miyamoto Y, Itoh K. 16S rRNA gene sequence-based analysis of clostridia related to conversion of germfree mice to the normal state. J Appl Microbiol. 2009;107(6):2088–97.
Article
CAS
Google Scholar
De Hertogh G, Aerssens J, de Hoogt R, Peeters P, Verhasselt P, Van Eyken P, Ectors N, Vermeire S, Rutgeerts P, Coulie B, et al. Validation of 16S rDNA sequencing in microdissected bowel biopsies from Crohn's disease patients to assess bacterial flora diversity. J Pathol. 2006;209(4):532–9.
Article
Google Scholar
Beneke T, Madden R, Makin L, Valli J, Sunter J, Gluenz E. A CRISPR Cas9 high-throughput genome editing toolkit for kinetoplastids. R Soc Open Sci. 2017;4(5):170095.
Article
Google Scholar
Comfort N. Genome editing: That's the way the CRISPR crumbles. Nature. 2017;546(7656):30–1.
Article
CAS
Google Scholar
Hryhorowicz M, Lipinski D, Zeyland J, Slomski R. CRISPR/Cas9 immune system as a tool for genome engineering. Arch Immunol Ther Exp. 2017;65(3):233–40.
Article
CAS
Google Scholar
Rath D, Amlinger L, Rath A, Lundgren M. The CRISPR-Cas immune system: biology, mechanisms and applications. Biochimie. 2015;117:119–28.
Article
CAS
Google Scholar
Overmann J, Coolen MJ, Tuschak C. Specific detection of different phylogenetic groups of chemocline bacteria based on PCR and denaturing gradient gel electrophoresis of 16S rRNA gene fragments. Arch Microbiol. 1999;172(2):83–94.
Article
CAS
Google Scholar
Zhan XY, Hu CH, Zhu QY. Targeting single-nucleotide polymorphisms in the 16S rRNA gene to detect and differentiate legionella pneumophila and non-legionella pneumophila species. Arch Microbiol. 2016;198(6):591–4.
Article
CAS
Google Scholar
Ravasi DF, Peduzzi S, Guidi V, Peduzzi R, Wirth SB, Gilli A, Tonolla M. Development of a real-time PCR method for the detection of fossil 16S rDNA fragments of phototrophic sulfur bacteria in the sediments of Lake Cadagno. Geobiology. 2012;10(3):196–204.
Article
CAS
Google Scholar
Parikh HI, Koparde VN, Bradley SP, Buck GA, Sheth NU. MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing. Bmc Bioinformatics. 2016;17(1):491.
Article
Google Scholar
Hua G, Cheng Y, Kong J, Li M, Zhao Z. High-throughput sequencing analysis of bacterial community spatiotemporal distribution in response to clogging in vertical flow constructed wetlands. Bioresour Technol. 2018;248:104–112.
Article
CAS
Google Scholar
Karapetsas A, Vavoulidis E, Galanis A, Sandaltzopoulos R, Kourkoutas Y. Rapid detection and identification of probiotic Lactobacillus casei ATCC 393 by multiplex PCR. J Mol Microb Biotech. 2010;18(3):156–61.
Article
CAS
Google Scholar
Wang B, Li JS, Li QR, Zhang HY, Li N. Isolation of adhesive strains and evaluation of the colonization and immune response by Lactobacillus plantarum L2 in the rat gastrointestinal tract. Int J Food Microbiol. 2009;132(1):59–66.
Article
CAS
Google Scholar
Conlee KM, Stephens ML, Rowan AN, King LA. Carbon dioxide for euthanasia: concerns regarding pain and distress, with special reference to mice and rats. Lab Anim. 2005;39(2):137–61.
Article
CAS
Google Scholar