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Nazir, Farzana, 2023. Microbial diversity in Swedish breeds of sheep analysed by amplicon based sequencing. Second cycle, A2E. Uppsala: SLU, Dept. of Anatomy, Physiology and Biochemistry

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Abstract

The gastrointestinal tract (GIT) of ruminants have divergent type of microbiome
provides favourable environment for their growth. In many species, these
microbiome considered as important source of assessing animal health & welfare.
A total of 18 different Swedish sheep breeds (n = 15) and Landrace Goats as an out
group (n = 3) were selected to examine the faecal microbiome, i.e., Rye (n=6),
Gestrike (n=4), Roslag (n=3), and Cross-breed (Suffolk + Texel) (n=2) & Goat
(n=3). The replicates of 32 faecal samples were subjected to DNA extraction, the
gel electrophoresis method, and amplification for PCR products and mixing. The
positive replicates of all extracted DNA samples were subjected to16s amplicon
metagenomics coupled with next generation sequencing (Illumina), quality control
(QC), and generated processed reads of total (1799435) for all bacteria and archaea.
The total of (10734) amplicon sequence variants (ASV) after the filtration were
employed for the phylogeny and taxonomy analysis of bacteria at the phylum and
genus level. Bioinformatics and statistical analysis was done by using DADA2
pipeline in the R software and PRISM software (Graphpad) for further visual
graphical presentation of data and compare the taxonomic classification.
The highest relative abundance was measured for Firmicute (66%) and
Bacteriodota (29%), Fibrobacteriota (1%), Proteobacteria (1%), and
Verrucomicrobiota (2%) among top 10 phyla. While, in the top 15 genera, the
highest relative abundance as shown in UCG-005 (24%), Rikenellaceae RC9 gut
group (13%), Christensenellaceae R-7 group (12%), Bacteroides (8%),
Monoglobus (6%), Alistipes (6%), Prevotellaceae UCG-004 (6%), Ruminococcus
(5%), Akkermansia (4%) and Lachnospiraceae AC2044 group (5%). Bray–Curtis
distances by Breed (PCoA and NMDS) showed clear difference in the clustering of
sheep from goat samples and PERMANOVA showed significance results (P<0.05)
but no significance difference were seen within different Swedish sheep breeds
according to ANOVA and Tukeys test.
This research is the first non-culture-based study to analyse the similarities and
dissimilarities of the faecal microbiome by using 16S amplicon based
metagenomics coupled with NGS (next generation sequencing) in different Swedish
breeds of sheep and goat (outgroup).

Main title:Microbial diversity in Swedish breeds of sheep analysed by amplicon based sequencing
Authors:Nazir, Farzana
Supervisor:Pelve, Erik and Johansson, Anna Maria
Examiner:Dicksved, Johan
Series:UNSPECIFIED
Volume/Sequential designation:UNSPECIFIED
Year of Publication:2023
Level and depth descriptor:Second cycle, A2E
Student's programme affiliation:VM006 Animal Science - Master's Programme
Supervising department:(VH) > Dept. of Anatomy, Physiology and Biochemistry
Keywords:Ruminants, Microbiome, NGS, Bioinformatics, Statistical Analysis, Metagenomics, Data Analysis
URN:NBN:urn:nbn:se:slu:epsilon-s-18568
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-s-18568
Subject. Use of subject categories until 2023-04-30.:Animal genetics and breeding
Language:English
Deposited On:26 Jan 2023 06:52
Metadata Last Modified:27 Jan 2023 02:01

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