Characterization and predictive functional profiles on metagenomic 16S rRNA data of liver transplant recipients: A longitudinal study

Abstract

Long-term survival after Liver Transplantation (LT) is often compromised by infectious and metabolic complications. We aimed to delineate alterations in intestinal microbiome (IM) over time that could contribute to medical complications compromising long-term survival following LT. Fecal samples from LT recipients were collected at 3 months (3 M) and 6 months (6 M) post-LT. The bacterial DNA was extracted using E.Z.N.A. Stool DNA Kit and 16S rRNA gene sequencing at V4 hypervariable region was performed. DADA2 and Phyloseq was implemented to analyze the taxonomic composition. Differentially abundant taxa were identified by metagenomeSeq and LEfSe.Piphillin, an Inferred functional metagenomic analysis tool was used to study the bacterial functional content. For comparison, healthy samples were extracted from NCBI and analyzed similarly. The taxonomic & functional profiles of LT recipients were validated with metagenomic sequencing data from animals exposed to immunosuppressants using Venny. Our findings provide a new perspective on longitudinal increase in specific IM communities post-LT along with an increase in bacterial genes associated with metabolic and infectious disease.

CONSORT-Characteristics and metabolic phenotype of gut microbiota in NAFLD patients

“…The incidence of NAFLD has increased significantly in recent years and has become a major cause of chronic liver disease worldwide, affecting human health adversely. [ 9 , 10 ] In view of the gut-liver axis concept, gut microbiota has emerged as a crucial topic in liver disease research and demonstrated its impact on the occurrence and development of chronic liver disease. Despite advances in the gut microbiota macrogenomics, the characteristics of the NAFLD gut microbiota and its metabolites have not been fully defined.…”

Lactobacillus rhamnosus GG supernatant promotes intestinal mucin production through regulating 5-HT4R and gut microbiota

“…Fecal DNA was extracted from stool samples using an E.Z.N.A. ® Stool DNA Kit (Omega Bio-Tek, USA) 35 following the manufacturer's guidelines. Specific primers (F341: ACTCCTACG GGRSGCAGCAG, R806: GGACTACVVGGGTATCTAATC) with barcodes targeting the V3-V4 hypervariable region of the 16S rRNA gene were used for PCR amplification in triplicate.…”

Pharmacomicrobiomics of Classical Immunosuppressant Drugs: A Systematic Review

“…After excluding the publications not complying with inclusion criteria, 86 records were considered suitable for full-text analysis. After reading these papers and examining their content the two reviewers identified 50 papers [ 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 ,…”

“…The main findings of the selected studies were summarized in a narrative form in the text of the article and in two tables, the first ( Table 1 ) concerning the papers on the effect of the intestinal microbiota on cIMDs [ 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 ], and the second ( Table 2 ) concerning the papers on effect of cIMDs on intestinal microbiota [ 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 ,…”