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Introduction to Cells, DNA, and Viruses
Published in Patricia G. Melloy, Viruses and Society, 2023
The remnants of viruses integrated into host genomes, called endogenous viral elements (EVEs), have been found in many different prokaryotic and eukaryotic genomes, including ours. Although typically small, extremely large EVEs, over a million nucleotide base pairs in length, have recently been identified in green algae. Scientists believe that these integrated viral genes may play a larger role in eukaryotic genome evolution than once thought (Moniruzzaman et al. 2020).
Evolution
Published in Paul Pumpens, Single-Stranded RNA Phages, 2020
Thus, according to Bollback and Huelsenbeck (2001), the ancestral phage genome increased in size on the order of 600 nucleotides after the divergence of the Allolevivirus and Levivirus lineages, but before the diversification of the Allolevivirus lineage, by either recombination or intramolecular duplication. A number of additional changes appeared to have been coupled with this genome expansion: notably, the loss of the lysis coding region, the evolution of a novel readthrough protein, and an increase in translation of the maturation protein. An increase in the genome size might be implicated in catalyzing all of these changes via changing the secondary structure of the RNA molecule. The lack of the lysis gene in the Allolevivirus was compensated for by the higher levels of the maturation protein which functioned in the phage release. Although the genome evolution in viruses was typically believed to be characterized by an economization of the genome, Bollback and Huelsenbeck (2001) indicated that increases in genome size might have played an important role in viral evolution.
Molecular Analysis of Plant DNA Genomes: Conserved and Diverged DNA Sequences
Published in S. K. Dutta, DNA Systematics, 2019
The plant genome is a complex form with a very high evolutionary lability. The genome evolution rate was higher in plants than in the other groups of higher eukaryotes studied. The rate of evolution was influenced by a specific evolutionary factor pervasive in the plant kingdom — polyploidy.
High throughput genome scale modeling predicts microbial vitamin requirements contribute to gut microbiome community structure
Published in Gut Microbes, 2022
Juan P. Molina Ortiz, Mark Norman Read, Dale David McClure, Andrew Holmes, Fariba Dehghani, Erin Rose Shanahan
The collective of self-organized microbes living in the human gut give rise to biological processes that modulate non-communicable disease (NCD) etiology.1–5 Gut strains adapt to the gut environment based on the metabolic attributes encoded in their genome. Molecules central to cell metabolism are considered essential nutrients when they must be provided by the environment. However, specific metabolic attributes allow strains the option of synthesizing such molecules when unavailable (optional nutrients). Such characteristics lead to the establishment of nutritional and bioenergetic exchanges between sets of strains with complementary metabolic attributes, resulting in the emergence of higher scales of community organization (higher order units). It is now understood that the microbial processes that influence human biology cannot be effectively explained by individual strains, but rather the resulting higher order units.6–8 These may take the form of specific co-abundance or interaction modules (IMs),6–8 or reflect broader aspects of microbial community assembly observed across human populations (such as community types or enterotypes)9,10 which likely represent differential nutritional and bioenergetic signatures.11 Although the mechanisms through which resources are exchanged have been described,12,13 and these can be readily related to genome evolution,14 the higher-order processes constraining emergent structures are yet to be defined, partially due to the inherent complexity within the community.
Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health
Published in Gut Microbes, 2021
Jessica C. Ezeji, Daven K. Sarikonda, Austin Hopperton, Hailey L. Erkkila, Daniel E. Cohen, Sandra P. Martinez, Fabio Cominelli, Tomomi Kuwahara, Armand E. K. Dichosa, Caryn E. Good, Michael R. Jacobs, Mikhail Khoretonenko, Alida Veloo, Alexander Rodriguez-Palacios
According to phylogenetic analyses, P. distasonis diverged from a common ancestor shared with Bacteroides species, as confirmed via nucleotide sequencing of the complete 16S rRNA gene from distinct bacterial species.37 A study by Xu et al.37 explored the driving forces behind the adaptation of Bacteroidetes in the distal gut environment and their importance to the evolution of human gut commensals. To examine how the intestinal environment affects microbial genome evolution, Xu et al.37 sequenced the genomes of two members of the distal human gut microbiota, B. vulgatus and P. distasonis. Through comparison with other sequenced gut and non-gut Bacteroidetes, and analyzing their niches and habitat adaptations, Xu et al. identified three general functions that could illustrate an evolutionary uniqueness for the Bacteroidetes phylum: polysaccharide metabolism, environmental sensing and gene regulation, and membrane transport. These processes are important in aiding with lateral gene transfer, mobile elements, and gene amplification, all of which affect the ability of gut-dwelling Bacteroidetes to vary their cell surface, sense their environment, and harvest nutrients present in the distal colon.37 More recently, genome-based analyses have examined the metabolic features that are typical for a wide array of Bacteroides, which complements the taxonomic classification of the phylumspecies within.38–40
Imaging the in vivo growth patterns of bacteria in human gut Microbiota
Published in Gut Microbes, 2021
Liyuan Lin, Jia Song, Jian Li, Xiaolei Zuo, Hong Wei, Chaoyong Yang, Wei Wang
It has been reported that strains of Lactobacillus reuteri in the mouse gut are genetically very different from those found in humans and have evolved various genes to facilitate their adaptation to the hosts.20,21 It’s, therefore, reasonable to speculate that the divergent trends of genome evolution in mouse and human gut microbiota may be responsible for the varied morphologies of the same species observed in different hosts. The differences in the physiology and immunity of hosts, such as the pH values of intestine, the level of oxygen tension, and the glycan profiles of mucus, were possible to promote this host-specific adaptation. Currently, studies on gut microbiota from different hosts relies on DNA sequencing to analyze the changes in overall microbial compositions.9,10,22 To the best of our knowledge, this is the first report on the morphological differences of gut microbes in different mammalian hosts. This may partially explain why the physiological and pathological functions of certain gut bacteria in mouse could not be reproducible in human studies.