Lifesequencing

Valencia, Spain

Lifesequencing

Valencia, Spain
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Belda E.,University of Valencia | Belda E.,Polytechnic University of Valencia | Belda E.,French Atomic Energy Commission | Pedrola L.,Lifesequencing | And 8 more authors.
PLoS ONE | Year: 2011

Background: Insects are associated with microorganisms that contribute to the digestion and processing of nutrients. The European Corn Borer (ECB) is a moth present world-wide, causing severe economical damage as a pest on corn and other crops. In the present work, we give a detailed view of the complexity of the microorganisms forming the ECB midgut microbiota with the objective of comparing the biodiversity of the midgut-associated microbiota and explore their potential as a source of genes and enzymes with biotechnological applications. Methodological/Principal Findings: A high-throughput sequencing approach has been used to identify bacterial species, genes and metabolic pathways, particularly those involved in plant-matter degradation, in two different ECB populations (field-collected vs. lab-reared population with artificial diet). Analysis of the resulting sequences revealed the massive presence of Staphylococcus warneri and Weissella paramesenteroides in the lab-reared sample. This enabled us to reconstruct both genomes almost completely. Despite the apparently low diversity, 208 different genera were detected in the sample, although most of them at very low frequency. By contrast, the natural population exhibited an even higher taxonomic diversity along with a wider array of cellulolytic enzyme families. However, in spite of the differences in relative abundance of major taxonomic groups, not only did both metagenomes share a similar functional profile but also a similar distribution of non-redundant genes in different functional categories. Conclusions/Significance: Our results reveal a highly diverse pool of bacterial species in both O. nubilalis populations, with major differences: The lab-reared sample is rich in gram-positive species (two of which have almost fully sequenced genomes) while the field sample harbors mainly gram-negative species and has a larger set of cellulolytic enzymes. We have found a clear relationship between the diet and the midgut microbiota, which reveals the selection pressure of food on the community of intestinal bacteria. © 2011 Belda et al.


Philadelphia, PA, December 6, 2016 - Endometrial microbiota (bacteria in the uterine cavity) play an important role in determining whether women are able to get pregnant via in vitro fertilization (IVF), according to a new study published in the American Journal of Obstetrics and Gynecology. "The uterine cavity has been considered sterile," explained lead investigator Carlos Simón, MD, PhD, of Igenomix Spain, and the Department of Obstetrics and Gynecology of the University of Valencia, Spain. "Our team sought to test the existence of endometrial microbiota that differs from that of the vagina. We assessed its hormonal regulation and analyzed the impact of the endometrial microbial community on reproductive outcome in patients undergoing IVF." To identify the existence of an endometrial microbiota, investigators evaluated paired samples of endometrial and vaginal fluid obtained from 13 fertile women in pre-receptive and receptive phases within the same menstrual cycle. To investigate the hormonal regulation of the endometrial microbiota during the acquisition of endometrial receptivity, endometrial fluid was collected at pre-receptive and receptive phases within the same cycle from 22 fertile women. Finally, the reproductive impact of an altered endometrial microbiota in endometrial fluid was assessed by implantation, ongoing pregnancy, and live birth rates in 35 infertile patients undergoing IVF with a receptive endometrium diagnosed using the endometrial receptivity array based on gene expression. When paired endometrial fluid and vaginal fluid samples from the same patients were examined, different bacterial communities were detected between the two sites in some women. The microbiota in the endometrial fluid was classified as Lactobacillus-dominated or non-Lactobacillus-dominated microbiota. There was no evidence that steroid hormones played a role in determining the composition of the microbial community in the endometrium. On the other hand, women with a non-Lactobacillus-dominated microbiota and a receptive endometrium had a significantly lower rate of implantation, pregnancy, and live birth than patients with a Lactobacillus-dominated microbiota. In an accompanying commentary, Linda C. Giudice, MD, PhD, Distinguished Professor and reproductive endocrinologist at the University of California San Francisco, noted that reproductive success is clearly not solely defined by endometrial histology and gene expression. The ongoing revolution in technology, multiple -omics, and multidimensional data analysis has opened the window of implantation to a greater level of scrutiny. It is time to investigate the endometrial microbiome and expand research to its virome, fungome, epigenome, and metabolome, she wrote. Putting the significance of this study into perspective, Roberto Romero, MD, DMedSci, Chief of the Perinatology Research Branch of NICHD/NIH and Editor-in-Chief for Obstetrics of the American Journal of Obstetrics and Gynecology, commented that "the endometrial cavity is not sterile and normally contains bacteria; however, whether bacteria within the cavity play a role in successful reproduction has been unknown to this point. The pioneering work of the team of Professor Simón now shows, for the first time, that colonization of the uterine cavity with some bacteria (non Lactobacillus-dominated) affects the success of in vitro fertilization, pregnancy rates, and live births. This brings hope that diagnostic tests to examine the microbial composition of the uterine cavity may be valuable in assessing the likelihood of success of IVF. Moreover, it raises the question of whether targeted treatment with antimicrobial agents or probiotics may be useful in improving reproductive success, and suggests that successful reproduction may depend on a host-microbial relationship in the endometrial cavity, unknown before this time." In addition to Igenomix and Valencia University, Lifesequencing and Biopolis (Scientific Park of Valencia University) contributed to this study. Endometrial samples were obtained from patients from IVI Valencia.


Wu G.A.,U.S. Department of Energy | Prochnik S.,U.S. Department of Energy | Jenkins J.,HudsonAlpha Institute for Biotechnology | Salse J.,French National Institute for Agricultural Research | And 65 more authors.
Nature Biotechnology | Year: 2014

Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes-a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes-and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement. © 2014 Nature America, Inc.

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