Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients
Publication Date
January 31, 2018
Authors
Ibrahim Hamad, Rita Abou Abdallah, Isabelle Ravaux, Saadia Mokhtari, et al
Volume
13
Issue
1
Pages
e0191913
DOI
https://dx.plos.org/10.1371/journal.pone.0191913
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0191913
Scopus
85041183268
Mendeley
http://www.mendeley.com/research/metabarcoding-analysis-eukaryotic-microbiota-gut-hivinfected-patients
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Mendeley | Further Information

{"title"=>"Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients", "type"=>"journal", "authors"=>[{"first_name"=>"Ibrahim", "last_name"=>"Hamad", "scopus_author_id"=>"55598341800"}, {"first_name"=>"Rita Abou", "last_name"=>"Abdallah", "scopus_author_id"=>"57193844671"}, {"first_name"=>"Isabelle", "last_name"=>"Ravaux", "scopus_author_id"=>"6603036399"}, {"first_name"=>"Saadia", "last_name"=>"Mokhtari", "scopus_author_id"=>"16317023000"}, {"first_name"=>"Hervé", "last_name"=>"Tissot-Dupont", "scopus_author_id"=>"7004136755"}, {"first_name"=>"Caroline", "last_name"=>"Michelle", "scopus_author_id"=>"26537832600"}, {"first_name"=>"Andreas", "last_name"=>"Stein", "scopus_author_id"=>"56346234600"}, {"first_name"=>"Jean Christophe", "last_name"=>"Lagier", "scopus_author_id"=>"24366829400"}, {"first_name"=>"Didier", "last_name"=>"Raoult", "scopus_author_id"=>"55144875700"}, {"first_name"=>"Fadi", "last_name"=>"Bittar", "scopus_author_id"=>"24376223400"}], "year"=>2018, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"620393478", "doi"=>"10.1371/journal.pone.0191913", "issn"=>"19326203", "scopus"=>"2-s2.0-85041183268", "sgr"=>"85041183268", "isbn"=>"1111111111"}, "id"=>"ef4ca4f3-c9e4-3be9-abc7-e77451d8a022", "abstract"=>"Research on the relationship between changes in the gut microbiota and human disease, including AIDS, is a growing field. However, studies on the eukaryotic component of the intestinal microbiota have just begun and have not yet been conducted in HIV-infected patients. Moreover, eukaryotic community profiling is influenced by the use of different methodologies at each step of culture-independent techniques. Herein, initially, four DNA extraction protocols were compared to test the efficiency of each method in recovering eukaryotic DNA from fecal samples. Our results revealed that recovering eukaryotic compo-nents from fecal samples differs significantly among DNA extraction methods. Subse-quently, the composition of the intestinal eukaryotic microbiota was evaluated in HIV-infected patients and healthy volunteers through clone sequencing, high-throughput sequencing of nuclear ribosomal internal transcribed spacers 1 (ITS1) and 2 (ITS2) ampli-cons and real-time PCRs. Our results revealed that not only richness (Chao-1 index) and alpha diversity (Shannon diversity) differ between HIV-infected patients and healthy volun-teers, depending on the molecular strategy used, but also the global eukaryotic community composition, with little overlapping taxa found between techniques. Moreover, our results based on cloning libraries and ITS1/ITS2 metabarcoding sequencing showed significant dif-ferences in fungal composition between HIV-infected patients and healthy volunteers, but without distinct clusters separating the two groups. Malassezia restricta was significantly more prevalent in fecal samples of HIV-infected patients, according to cloning libraries, whereas operational taxonomic units (OTUs) belonging to Candida albicans and Candida tropicalis were significantly more abundant in fecal samples of HIV-infected patients com-pared to healthy subjects in both ITS subregions. Finally, real-time PCR showed the pres-ence of Microsporidia, Giardia lamblia, Blastocystis and Hymenolepis diminuta in different proportions in fecal samples from HIV patients as compared to healthy individuals. Our work revealed that the use of different sequencing approaches can impact the perceived eukary-otic diversity results of the human gut. We also provide a more comprehensive view of the eukaryotic community in the gut of HIV-infected patients through the complementarity of the", "link"=>"http://www.mendeley.com/research/metabarcoding-analysis-eukaryotic-microbiota-gut-hivinfected-patients", "reader_count"=>15, "reader_count_by_academic_status"=>{"Researcher"=>4, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>2, "Student > Master"=>1, "Student > Bachelor"=>2, "Unspecified"=>2}, "reader_count_by_user_role"=>{"Researcher"=>4, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>2, "Student > Master"=>1, "Student > Bachelor"=>2, "Unspecified"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Engineering"=>1, "Agricultural and Biological Sciences"=>5, "Medicine and Dentistry"=>2, "Immunology and Microbiology"=>1, "Biochemistry, Genetics and Molecular Biology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>5}}, "group_count"=>0}

Scopus | Further Information

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