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First Complete Genome Sequences of Janthinobacterium lividum EIF1 and EIF2 and Their Comparative Genome Analysis
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Age of the association between Helicobacter pylori and man
Get PDFWhen modern humans left Africa ca. 60,000 years ago (60 kya), they were already infected with Helicobacter pylori, and these bacteria have subsequently diversified in parallel with their human hosts. But how long were humans infected by H. pylori prior to the out-of-Africa event? Did this co-evolution predate the emergence of modern humans, spanning the species divide? To answer these questions, we investigated the diversity of H. pylori in Africa, where both humans and H. pylori originated. Three distinct H. pylori populations are native to Africa: hpNEAfrica in Afro-Asiatic and Nilo-Saharan speakers, hpAfrica1 in Niger-Congo speakers and hpAfrica2 in South Africa. Rather than representing a sustained co-evolution over millions of years, we find that the coalescent for all H. pylori plus its closest relative H. acinonychis dates to 88–116 kya. At that time the phylogeny split into two primary super-lineages, one of which is associated with the former hunter-gatherers in southern Africa known as the San. H. acinonychis, which infects large felines, resulted from a later host jump from the San, 43–56 kya. These dating estimates, together with striking phylogenetic and quantitative human-bacterial similarities show that H. pylori is approximately as old as are anatomically modern humans. They also suggest that H. pylori may have been acquired via a single host jump from an unknown, non-human host. We also find evidence for a second Out of Africa migration in the last 52,000 years, because hpEurope is a hybrid population between hpAsia2 and hpNEAfrica, the latter of which arose in northeast Africa 36–52 kya, after the Out of Africa migrations around 60 kya
Dynamic Interactions Between Mega Symbiosis ICEs and Bacterial Chromosomes Maintain Genome Architecture
Get PDFAcquisition of mobile genetic elements can confer novel traits to bacteria. Some integrative and conjugative elements confer upon members of Bradyrhizobium the capacity to fix nitrogen in symbiosis with legumes. These so-called symbiosis integrative conjugative elements (symICEs) can be extremely large and vary as monopartite and polypartite configurations within chromosomes of related strains. These features are predicted to impose fitness costs and have defied explanation. Here, we show that chromosome architecture is largely conserved despite diversity in genome composition, variations in locations of attachment sites recognized by integrases of symICEs, and differences in large-scale chromosomal changes that occur upon integration. Conversely, many simulated nonnative chromosome–symICE combinations are predicted to result in lethal deletions or disruptions to architecture. Findings suggest that there is compatibility between chromosomes and symICEs. We hypothesize that the size and structural flexibility of symICEs are important for generating combinations that maintain chromosome architecture across a genus of nitrogen-fixing bacteria with diverse and dynamic genomes
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Complete genomes of symbiotic cyanobacteria clarify the evolution of Vanadium-nitrogenase
Get PDFPlant endosymbiosis with nitrogen-fixing cyanobacteria has independently evolved in diverse plant lineages, offering a unique window to study the evolution and genetics of plant-microbe interaction. However, very few complete genomes exist for plant cyanobionts, and therefore little is known about their genomic and functional diversity. Here, we present four complete genomes of cyanobacteria isolated from bryophytes. Nanopore long-read sequencing allowed us to obtain circular contigs for all the main chromosomes and most of the plasmids. We found that despite having a low 16S rRNA sequence divergence, the four isolates exhibit considerable genome reorganizations and variation in gene content. Furthermore, three of the four isolates possess genes encoding vanadium (V)-nitrogenase (vnf), which is uncommon among diazotrophs and has not been previously reported in plant cyanobionts. In two cases, the vnf genes were found on plasmids, implying possible plasmid-mediated horizontal gene transfers. Comparative genomic analysis of vnf-containing cyanobacteria further identified a conserved gene cluster. Many genes in this cluster have not been functionally characterized and would be promising candidates for future studies to elucidate V-nitrogenase function and regulation
Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux
Get PDFCitrobacter rodentium is a natural mouse pathogen that causes attaching and effacing (A/E) lesions. It shares a common virulence strategy with the clinically significant human A/E pathogens enteropathogenic E. coli (EPEC) and enterohaemorrhagic E. coli (EHEC) and is widely used to model this route of pathogenesis. We previously reported the complete genome sequence of C. rodentium ICC168, where we found that the genome displayed many characteristics of a newly evolved pathogen. In this study, through PFGE, sequencing of isolates showing variation, whole genome transcriptome analysis and examination of the mobile genetic elements, we found that, consistent with our previous hypothesis, the genome of C. rodentium is unstable as a result of repeat-mediated, large-scale genome recombination and because of active transposition of mobile genetic elements such as the prophages. We sequenced an additional C. rodentium strain, EX-33, to reveal that the reference strain ICC168 is representative of the species and that most of the inactivating mutations were common to both isolates and likely to have occurred early on in the evolution of this pathogen. We draw parallels with the evolution of other bacterial pathogens and conclude that C. rodentium is a recently evolved pathogen that may have emerged alongside the development of inbred mice as a model for human disease
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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It's a Gut Feeling: The Gut Microbiome and Depression
Get PDFMajor depressive disorder is one of the primary causes of disability worldwide. The
disorder involves dysfunction of the brain-gut axis, which refers to the chemical and
physical interactions between the brain and the gut. Abnormal gut microbiota
composition may cause this dysfunction, in turn causing depression, whereas
restoration of such disturbances may alleviate symptoms of the disorder. Current
depression research investigates the brain-gut-microbiota axis, and studies indicate
that proper functioning of this axis may aid in the prevention and therapy of this
disorder.Integrative Biolog
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A reevaluation of the phylogenetic tree for the genus Homo: a reclassification based on contemporary evidence
Get PDFThere is considerable variation in the proposed taxonomic and phylogenetic hypotheses for the genus Homo. This is due to the limitations of the hominin fossil record; morphological data are the most available, as genetic material is less likely to be preserved over large timescales and varying environments. The taxonomic hypotheses fall into two broad categories: lumping taxonomies tend to incorporate many fossil groups into one species, and splitting taxonomies tend to split discovered populations into numerous species. The availability of information on the morphology and genetics of different archaic human species continues to change as data extraction and processing techniques improve, and new species definitions also develop to accommodate evolution in different contexts. This then influences the validity of different taxonomic hypotheses, as well as the phylogenies that incorporate them. Here I evaluated the genetic, morphometric, and probabilistic analyses that have been conducted for different fossils in the genus Homo, and proposed a phylogeny and taxonomy that are most consistent with recent fossil discoveries and advances in the field of evolutionary biology. I analyzed the different fossil specimens that are attributed to H. habilis, H. erectus, and H. sapiens under the most conservative taxonomic hypothesis, and proceeded to reclassify fossils in order to achieve consistency with the current data. I classify H. rudolfensis as a subspecies of H. habilis, and have placed H. antecessor and H. ergaster as subspecies of H. erectus. The rest of the species in the proposed phylogeny are H. floresiensis, H. luzonensis, H. naledi, H. heidelbergensis, H. neanderthalensis, H. denisova, and H.sapiens. H. naledi is classified as a descendent of H. erectus, as the H. erectus-H. naledi pairwise comparisons showed the least divergence for the majority of craniodental traits studied. H. floresiensis and H. luzonensis have also been placed as descendants of H. erectus, due to similarities in dental surface and cranial size trends. Additionally, H. heidelbergensis is designated as the last common ancestor for Neanderthals, Denisovans, and modern humans, owing to trends across several fossils suggesting a relatively large-brained and variable population that descended from H. erectus and spread into Europe. I also discussed the limitations of this phylogeny and potential for reclassification as more fossil data are collected.Integrative Biolog
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