Paredes, R. | Search bioRxiv

bioRxiv2018

Host genetic associations with the gut microbiota in HIV-1-infected subjects: a pilot exploratory study

The impact of host genetics on gut microbial dynamics is debated. No study to date has investigated the possible role of host genetics in shaping the gut microbiota in HIV-1 infected subjects. With the aim of generating preliminary data to inform future host genetic studies, we performed an exploratory host exome analysis of 147 subjects either infected or at risk of becoming infected with HIV-1 from the MetaHIV cohort in Barcelona. Using a DNA microarray chip, we sought to identify host genetic variants associated to three specific microbial features with a potentially inheritable component, and which were previously found to be associated with gut dysbiosis in HIV infection, i.e.: gut enterotype, presence of methanogenic archaea and microbial gene richness. After correction for multiple comparisons, we did not observe any statistically significant association between the hosts genetic landscape and the explored gut microbiome traits. These findings will help design future, adequately-powered studies to assess the influence of host genetics in the microbiome of HIV-1-infected subjects.

genomics↗

bioRxiv2018

New insights of the local immune response against both fertile and infertile hydatid cysts

BackgroundCystic echinococcosis is caused by the metacestode of the zoonotic flatworm Echinococcus granulosus. Within the viscera of the intermediate host, the metacestode grows as a unilocular cyst known as hydatid cyst. This cyst is comprised of two layers of parasite origin: germinal and laminated layers, and one of host origin: the adventitial layer, that encapsulates the parasite. This adventitial layer is composed of collagen fibers, epithelioid cells, eosinophils and lymphocytes. To establish itself inside the host, the germinal layer produces the laminated layer, and to continue its life cycle, generates protoscoleces. Some cysts are unable to produce protoscoleces, and are defined as infertile cysts. The molecular mechanisms involved in cyst fertility are not clear, however, the host immune response could play a crucial role.\n\nMethodology/Principal fidingsWe collected hydatid cysts from both liver and lungs of slaughtered cattle, and histological sections of fertile, infertile and small hydatid cysts were stained with haematoxylin-eosin. A common feature observed in infertile cysts was the disorganization of the laminated layer by the infiltration of host immune cells. These infiltrating cells eventually destroy parts of laminated layer. Immunohistochemical analysis of both parasite and host antigens, identify these cells as cattle macrophages and are present inside the cysts associated to germinal layer.\n\nConclusions/SignificanceThis is the first report that indicates to cell from immune system present in adventitial layer of infertile bovine hydatid cysts could disrupt the laminated layer, infiltrating and probably causing the infertility of cyst.\n\nAuthor SummaryCystic echinococcosis is caused by the zoonotic flatworm Echinococcus granulosus. Within the viscera of the intermediate host, mainly liver and lungs of herbivores such as cows and sheep as well as human beings, the parasite grows as a unilocular cyst known as hydatid cyst. These cysts develop in their inner chamber a structure known as protoscolex, when consumed by the definitive host (e.g. dogs), it grows into a worm that resides in the small intestine and produces eggs that contaminate the environment. In cattle, most hydatid cysts are unable to produce protoscoleces, and thus are termed infertile hydatid cysts. The molecular mechanisms that explain the causes of hydatid cyst infertility remain unknown. We routinely collected cattle hydatid cysts from both liver and lugs and processed them for histological analysis. We found that there is a subset of fertile hydatid cysts that have low protoscolex viability and high immune infiltration surrounding the cyst. All infertile cysts have high immune infiltration, and many of them show disruption of the laminated layer and immune cells of host origin inside the cyst. This is the first report that shows that the cyst can be infiltrated by the host immune system.

immunology↗

bioRxiv2017

Balances: a new perspective for microbiome analysis

High-throughput sequencing technologies have revolutionized microbiome research by allowing the relative quantification of microbiome composition and function in different environments. One of the main goals in microbiome analysis is the identification of microbial species that are differentially abundant among groups of samples, or whose abundance is associated with a variable of interest. Most available methods for microbiome abundance testing perform univariate tests for each microbial species or taxa separately, ignoring the compositional nature of microbiome data.\n\nWe propose an alternative approach for microbiome abundance testing that consists on the identification of two groups of taxa whose relative abundance, or balance, is associated with the response variable of interest. This approach is appealing, since it has direct translation to the biological concept of ecological balance between species in an ecosystem. In this work, we present selbal, a greedy stepwise algorithm for balance selection. We illustrate the algorithm with 16s abundance data from an HIV-microbiome study and a Crohn-microbiome study.\n\nImportanceA more meaningful approach for microbiome abundance testing is presented. Instead of testing each taxon separately we propose to explore abundance balances among groups of taxa. This approach acknowledges the compositional nature of microbiome data.

bioinformatics↗