Characterization of bacteria in biopsies of colon and stools by high throughput sequencing of the V2 region of bacterial 16S rRNA gene in human.
; Deffontaine Deurbroeck, Valérie ; Louis, Edouard et al
in PloS one (2011), 6(2), 16952
BACKGROUND: The characterization of the human intestinal microflora and their interactions with the host have been identified as key components in the study of intestinal disorders such as inflammatory ... [more ▼]
BACKGROUND: The characterization of the human intestinal microflora and their interactions with the host have been identified as key components in the study of intestinal disorders such as inflammatory bowel diseases. High-throughput sequencing has enabled culture-independent studies to deeply analyze bacteria in the gut. It is possible with this technology to systematically analyze links between microbes and the genetic constitution of the host, such as DNA polymorphisms and methylation, and gene expression. METHODS AND FINDINGS: In this study the V2 region of the bacterial 16S ribosomal RNA (rRNA) gene using 454 pyrosequencing from seven anatomic regions of human colon and two types of stool specimens were analyzed. The study examined the number of reads needed to ascertain differences between samples, the effect of DNA extraction procedures and PCR reproducibility, and differences between biopsies and stools in order to design a large scale systematic analysis of gut microbes. It was shown (1) that sequence coverage lower than 1,000 reads influenced quantitative and qualitative differences between samples measured by UniFrac distances. Distances between samples became stable after 1,000 reads. (2) Difference of extracted bacteria was observed between the two DNA extraction methods. In particular, Firmicutes Bacilli were not extracted well by one method. (3) Quantitative and qualitative difference in bacteria from ileum to rectum colon were not observed, but there was a significant positive trend between distances within colon and quantitative differences. Between sample type, biopsies or stools, quantitative and qualitative differences were observed. CONCLUSIONS: Results of human colonic bacteria analyzed using high-throughput sequencing were highly dependent on the experimental design, especially the number of sequence reads, DNA extraction method, and sample type. [less ▲]Detailed reference viewed: 12 (2 ULg)
Seasonal variation in molar outline of bank voles: An effect of wear?
; ; et al
in Mammalian Biology (2010)Detailed reference viewed: 23 (8 ULg)
A relict bank vole lineage highlights the biogeographic history of the Pyrenean region in Europe
Deffontaine Deurbroeck, Valérie ; ; Fontaine, Michaël et al
in Molecular Ecology (2009)
The Pyrenean region exhibits high levels of endemism suggesting a major contribution to the phylogeography of European species. But, to date, the role of the Pyrenees and surrounding areas as a glacial ... [more ▼]
The Pyrenean region exhibits high levels of endemism suggesting a major contribution to the phylogeography of European species. But, to date, the role of the Pyrenees and surrounding areas as a glacial refugium for temperate species remains poorly explored. In the current study, we investigated the biogeographic role of the Pyrenean region through the analyses of genetic polymorphism and morphology of a typical forest-dwelling small mammal, the bank vole (Myodes glareolus). Analyses of the mitochondrial cytochrome b gene and the third upper molar (M(3)) show a complex phylogeographic structure in the Pyrenean region with at least three distinct lineages: the Western European, Spanish and Basque lineages. The Basque lineage in the northwestern (NW) Pyrenees was identified as a new clearly differentiated and geographically localized bank vole lineage in Europe. The average M(3) shape of Basque bank voles suggests morphological differentiation but also restricted genetic exchanges with other populations. Our genetic and morphological results as well as palaeo-environmental and fossils records support the hypothesis of a new glacial refugium in Europe situated in the NW Pyrenees. The permissive microclimatic conditions that prevailed for a long time in this region may have allowed the survival of temperate species, including humans. Moreover, local differentiation around the Pyrenees is favoured by the opportunity for populations to track the shift of the vegetation belt in altitude rather than in latitude. The finding of the Basque lineage is in agreement with the high level of endemic taxa reported in the NW Pyrenees. [less ▲]Detailed reference viewed: 127 (19 ULg)
A northern glacial refugium for bank voles (Clethrionomys glareolus).
; Deffontaine Deurbroeck, Valérie ; et al
in Proceedings of the National Academy of Sciences of the United States of America (2006), 103(40), 14860-14864
There is controversy and uncertainty on how far north there were glacial refugia for temperate species during the Pleistocene glaciations and in the extent of the contribution of such refugia to present ... [more ▼]
There is controversy and uncertainty on how far north there were glacial refugia for temperate species during the Pleistocene glaciations and in the extent of the contribution of such refugia to present-day populations. We examined these issues using phylogeographic analysis of a European woodland mammal, the bank vole (Clethrionomys glareolus). A Bayesian coalescence analysis indicates that a bank vole population survived the height of the last glaciation (≈25,000–10,000 years B.P.) in the vicinity of the Carpathians, a major central European mountain chain well north of the Mediterranean areas typically regarded as glacial refugia for temperate species. Parameter estimates from the fitted isolation with migration model show that the divergence of the Carpathian population started at least 22,000 years ago, and it was likely followed by only negligible immigration from adjacent regions, suggesting the persistence of bank voles in the Carpathians through the height of the last glaciation. On the contrary, there is clear evidence for gene flow out of the Carpathians, demonstrating the contribution of the Carpathian population to the colonization of Europe after the Pleistocene. These findings are consistent with data from animal and plant fossils recovered in the Carpathians and provide the clearest phylogeographic evidence to date of a northern glacial refugium for temperate species in Europe. [less ▲]Detailed reference viewed: 21 (1 ULg)
Beyond the Mediterranean peninsulas: evidence of central European glacial refugia for a temperate forest mammal species, the bank vole (Clethrionomys glareolus).
Deffontaine Deurbroeck, Valérie ; Libois, Roland ; et al
in Molecular Ecology (2005), 14(6), 1727-1739
This study details the phylogeographic pattern of the bank vole, Clethrionomys glareolus, a European rodent species strongly associated with forest habitat. We used sequences of 1011 base pairs of the ... [more ▼]
This study details the phylogeographic pattern of the bank vole, Clethrionomys glareolus, a European rodent species strongly associated with forest habitat. We used sequences of 1011 base pairs of the mitochondrial DNA cytochrome b gene from 207 bank voles collected in 62 localities spread throughout its distribution area. Our results reveal the presence of three Mediterranean (Spanish, Italian and Balkan) and three continental (western, eastern and 'Ural') phylogroups. The endemic Mediterranean phylogroups did not contribute to the postglacial recolonization of much of the Palaearctic range of species. Instead, the major part of this region was apparently recolonized by bank voles that survived in glacial refugia in central Europe. Moreover, our phylogeographic analyses also reveal differentiated populations of bank voles in the Ural mountains and elsewhere, which carry the mitochondrial DNA of another related vole species, the ruddy vole (Clethrionomys rutilus). In conclusion, this study demonstrates a complex phylogeographic history for a forest species in Europe which is sufficiently adaptable that, facing climate change, survives in relict southern and northern habitats. The high level of genetic diversity characterizing vole populations from parts of central Europe also highlights the importance of such regions as a source of intraspecific genetic biodiversity. [less ▲]Detailed reference viewed: 32 (5 ULg)
Phylogeography of Harbour Porpoise (Phocoena phocoena) in the Eastern North Atlantic and in the Black Sea Explored by the Analyses of Nuclear and Mitochondrial DNA
; ; et al
Study of the genetic population structure and the demographic history of the harbour porpoise (Phocoena phocoena) has been nearly comprehensive throughout its distribution in North Atlantic, most studies ... [more ▼]
Study of the genetic population structure and the demographic history of the harbour porpoise (Phocoena phocoena) has been nearly comprehensive throughout its distribution in North Atlantic, most studies using the mitochondrial control region as a genetic marker. Although these studies have shown population structure in some parts of the North Atlantic, mitochondrial DNA is a single, maternally inherited locus and therefore insufficient to fully characterize population structure and history. Polymorphism at 11 microsatellite loci was analyzed in harbour porpoises collected throughout the range of the species in the Central and Eastern North Atlantic from the Iberian peninsula northward to Arctic waters (Portugal, Spain, bay of Biscay, Irish waters, English Channel, the southern bay of the North Sea, Norway, Faroe Islands, and Iceland) and also along the coasts of the Black Sea (Turkey, Ukraine, Bulgaria and Georgia). Multilocus tests for allele frequency differences and population structure estimates indicate complete genetic isolation between Atlantic and Black Sea porpoises. No fine population structure was observed within the Black Sea, and this population displayed a low genetic diversity compared to those of Atlantic. These results can be interpreted in the light of the demographic history of this relict population and the strong founder effect and bottleneck it may have undergone in its past evolution. In Eastern North Atlantic waters, microsatellite data revealed fine scale partitioning of the genetic variation. These results will be compared to the pattern previously reported based on the analysis of the mtDNA control region, and seem to correlate with variation in oceanographic features. [less ▲]Detailed reference viewed: 49 (5 ULg)
Comparative phylogeography of forest rodents (Apodemus sylvaticus, A. flavicollis and Clethrionomys glareolus) in the western Palearctic region: how the same quaternary climatic changes led to different evolutionary histories
; Deffontaine Deurbroeck, Valérie ; Libois, Roland
in Macholan, Milos; Bryja, Josef; Zima, Jan (Eds.) European Mammalogy 2003 (2003)Detailed reference viewed: 25 (5 ULg)