scholarly journals Deciphering Functional Redundancy in the Human Microbiome

2017 ◽  
Author(s):  
Liang Tian ◽  
Xu-Wen Wang ◽  
Ang-Kun Wu ◽  
Yuhang Fan ◽  
Jonathan Friedman ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Degree Distribution ◽  
Selection Pressure ◽  
Human Microbiome ◽  
Functional Redundancy ◽  
Taxonomic Composition ◽  
Gene Gain ◽  
Topological Features ◽  
Nested Structure

Although the taxonomic composition of the human microbiome varies tremendously across individuals, its gene composition or functional capacity is highly conserved1-5---implying an ecological property known as functional redundancy. Such functional redundancy is thought to underlie the stability and resilience of the human microbiome6,7, but its origin is elusive. Here, we investigate the basis for functional redundancy in the human microbiome by analyzing its genomic content network --- a bipartite graph that links microbes to the genes in their genomes. We show that this network exhibits several topological features, such as highly nested structure and fat-tailed gene degree distribution, which favor high functional redundancy. To explain the origins of these topological features, we develop a simple genome evolution model that explicitly considers selection pressure, and the processes of gene gain and loss, and horizontal gene transfer. We find that moderate selection pressure and high horizontal gene transfer rate are necessary to generate genomic content networks with both highly nested structure and fat-tailed gene degree distribution, and consequently favor high functional redundancy. These findings provide insights into the relationships between structure and function in complex microbial communities. This work elucidates the potential ecological and evolutionary processes that create and maintain functional redundancy in the human microbiome and contribute to its resilience.

scholarly journals Deciphering functional redundancy in the human microbiome

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Liang Tian ◽  
Xu-Wen Wang ◽  
Ang-Kun Wu ◽  
Yuhang Fan ◽  
Jonathan Friedman ◽  
...  
Keyword(s):  
Fecal Microbiota Transplantation ◽  
Human Microbiome ◽  
Functional Redundancy ◽  
Fecal Microbiota ◽  
Taxonomic Composition ◽  
Topological Features ◽  
Its Gene ◽  
The Stability ◽  
Stability And Resilience ◽  
Analyze Data

AbstractAlthough the taxonomic composition of the human microbiome varies tremendously across individuals, its gene composition or functional capacity is highly conserved — implying an ecological property known as functional redundancy. Such functional redundancy has been hypothesized to underlie the stability and resilience of the human microbiome, but this hypothesis has never been quantitatively tested. The origin of functional redundancy is still elusive. Here, we investigate the basis for functional redundancy in the human microbiome by analyzing its genomic content network — a bipartite graph that links microbes to the genes in their genomes. We find that this network exhibits several topological features that favor high functional redundancy. Furthermore, we develop a simple genome evolution model to generate genomic content network, finding that moderate selection pressure and high horizontal gene transfer rate are necessary to generate genomic content networks with key topological features that favor high functional redundancy. Finally, we analyze data from two published studies of fecal microbiota transplantation (FMT), finding that high functional redundancy of the recipient’s pre-FMT microbiota raises barriers to donor microbiota engraftment. This work elucidates the potential ecological and evolutionary processes that create and maintain functional redundancy in the human microbiome and contribute to its resilience.

scholarly journals Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae

2020 ◽  
Vol 12 (11) ◽  
pp. 2002-2014
Author(s):  
Ling-Ling Yang ◽  
Zhao Jiang ◽  
Yan Li ◽  
En-Tao Wang ◽  
Xiao-Yang Zhi
Keyword(s):  
Nitrogen Fixation ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Symbiotic Nitrogen Fixation ◽  
Gene Families ◽  
Time Span ◽  
Soil Conditions ◽  
Gene Gain ◽  
Nitrogen Fixing ◽  
Pan Genome

Abstract Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analyzed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using a phylogenomics approach. Intriguingly, although the genetic expansion that occurred in chromosomal regions was the main reason for the high proportion of low-frequency flexible gene families in the pan-genome, gene gain events associated with accessory plasmids introduced more genes into the genomes of nitrogen-fixing species. For symbiotic plasmids, although horizontal gene transfer frequently occurred, transfer may be impeded by, such as, the host’s physical isolation and soil conditions, even among phylogenetically close species. During coevolution with leguminous hosts, the plasmid system, including accessory and symbiotic plasmids, may have evolved over a time span, and provided rhizobial species with the ability to adapt to various environmental conditions and helped them achieve nitrogen fixation. These findings provide new insights into the phylogeny of Rhizobiaceae and advance our understanding of the evolution of symbiotic nitrogen fixation.

scholarly journals Elevated rates of horizontal gene transfer in the industrialized human microbiome

Cell ◽  
2021 ◽  
Author(s):  
Mathieu Groussin ◽  
Mathilde Poyet ◽  
Ainara Sistiaga ◽  
Sean M. Kearney ◽  
Katya Moniz ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Human Microbiome

scholarly journals Zoonotic Significance and Antimicrobial Resistance in Salmonella in Poultry in Bangladesh for the Period of 2011–2021

2021 ◽  
Vol 1 (1) ◽  
pp. 3-24
Author(s):  
Md. Jannat Hossain ◽  
Youssef Attia ◽  
Fatimah Muhammad Ballah ◽  
Md. Saiful Islam ◽  
Md. Abdus Sobur ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Antimicrobial Resistance ◽  
Horizontal Gene Transfer ◽  
Selection Pressure ◽  
Economic Loss ◽  
Multidrug Resistant ◽  
Foodborne Illness ◽  
The Status ◽  
Resistance Patterns ◽  
Effective Drugs

Antimicrobial resistance (AMR) in Salmonella in poultry poses a serious human health threat as it has zoonotic importance. Poultry is often linked with outbreaks of Salmonella-associated foodborne illness. Since antimicrobials are heavily used in poultry in Bangladesh, multidrug-resistant (MDR) Salmonella is quite frequently found there. MDR Salmonella is challenging to treat with antimicrobials and often causes a severe economic loss in the poultry sector. By horizontal gene transfer and/or evolutionary mutations, antimicrobials primarily exert selection pressure that contributes to antimicrobials resistance. In addition, resistance patterns can vary with variations in time and space. Without having prior knowledge of resistance patterns, no effective drugs could be prescribed. Therefore, it is crucial to have updated knowledge on the status of AMR in Salmonella in Bangladesh for effective treatment and management of the flocks against salmonellosis. There are several review articles on AMR in Salmonella in poultry in Bangladesh; they lack the whole scenario of the country and particularly do not have enough data on the poultry environment. Considering this scenario, in this review, we have focused on AMR in Salmonella in poultry in Bangladesh (2011–2021), with particular emphasis on data from the poultry and farm environments on a divisional zone basis.

scholarly journals Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1805 ◽  
Author(s):  
Eugene V. Koonin
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Trees ◽  
Point Mutations ◽  
Theoretical Models ◽  
Microbial Evolution ◽  
Gene Gain ◽  
Gene Trees ◽  
Ratchet Effect ◽  
Evolutionary Transitions

The wide spread of gene exchange and loss in the prokaryotic world has prompted the concept of ‘lateral genomics’ to the point of an outright denial of the relevance of phylogenetic trees for evolution. However, the pronounced coherence congruence of the topologies of numerous gene trees, particularly those for (nearly) universal genes, translates into the notion of a statistical tree of life (STOL), which reflects a central trend of vertical evolution. The STOL can be employed as a framework for reconstruction of the evolutionary processes in the prokaryotic world. Quantitatively, however, horizontal gene transfer (HGT) dominates microbial evolution, with the rate of gene gain and loss being comparable to the rate of point mutations and much greater than the duplication rate. Theoretical models of evolution suggest that HGT is essential for the survival of microbial populations that otherwise deteriorate due to the Muller’s ratchet effect. Apparently, at least some bacteria and archaea evolved dedicated vehicles for gene transfer that evolved from selfish elements such as plasmids and viruses. Recent phylogenomic analyses suggest that episodes of massive HGT were pivotal for the emergence of major groups of organisms such as multiple archaeal phyla as well as eukaryotes. Similar analyses appear to indicate that, in addition to donating hundreds of genes to the emerging eukaryotic lineage, mitochondrial endosymbiosis severely curtailed HGT. These results shed new light on the routes of evolutionary transitions, but caution is due given the inherent uncertainty of deep phylogenies.

scholarly journals Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss

2016 ◽  
Vol 33 (7) ◽  
pp. 1843-1857 ◽  
Author(s):  
Seyed Alireza Zamani-Dahaj ◽  
Mohamed Okasha ◽  
Jakub Kosakowski ◽  
Paul G. Higgs
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Gain ◽  
Gain And Loss ◽  
Phylogenetic Models

scholarly journals Quorum sensing-mediated inter-specific conidial anastomosis tube fusion between Colletotrichum gloeosporioides and C. siamense

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nikita Mehta ◽  
Abhishek Baghela
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Quorum Sensing ◽  
Selection Pressure ◽  
Lipid Droplets ◽  
Fungal Pathogens ◽  
Colletotrichum Gloeosporioides ◽  
Phenotypic Diversity ◽  
Quorum Sensing Molecule

AbstractMany plant pathogenic filamentous fungi undergo fusion of conidia through conidial anastomosis tubes (CATs), which is believed to facilitate horizontal gene transfer between species. We discovered a remarkable inter-specific CAT fusion between two important plant fungal pathogens Colletotrichum gloeosporioides and C. siamense. In an invitro assay, under no selection pressure, the inter-specific CAT fusion was preferred with higher frequency (25% ± 5%) than intra-specific CAT fusion (11% ± 3.6%). Different stages of CAT fusion viz. CAT induction, homing, and fusion were observed during this inter-specific CAT fusion. The CAT fusion was found to be higher in absence of nutrients and under physiological stresses. This CAT fusion involved a quorum sensing phenomenon, wherein the CAT induction was dependent on conidial density and the putative quorum sensing molecule was extractable in chloroform. Movement of nuclei, mitochondria, and lipid droplets were observed during the CAT fusion. Post CAT fusion, the resulting conidia gave rise to putative heterokaryotic progenies with variable colony characteristics as compared to their parental strains. Few heterokaryons showed variable AFLP banding pattern compared to their parental strains, thereby suggesting a possible genetic exchange between the two species through CAT fusion. The heterokaryotic progenies exhibited varied fitness under different stress conditions. Our study illustrated a possible role of inter-specific CAT fusion in generation of genetic and phenotypic diversity in these fungal pathogens.

scholarly journals Origins of major archaeal clades do not correspond to gene acquisitions from bacteria

2015 ◽  
Author(s):  
Mathieu Groussin ◽  
Bastien Boussau ◽  
Gergely Szöllősi ◽  
Laura Eme ◽  
Manolo Gouy ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Recent Article ◽  
Specific Gene ◽  
Gene Gain ◽  
Number Of Genes ◽  
Gain And Loss ◽  
Phylogenetic Models

In a recent article, Nelson-Sathi et al. [NS] report that the origins of Major Archaeal Lineages [MAL] correspond to massive group-specific gene acquisitions via horizontal gene transfer (HGT) from bacteria (Nelson-Sathi et al., 2015, Nature 517(7532):77-80). If correct, this would have fundamental implications for the process of diversification in microbes. However, a re-examination of these data and results shows that the methodology used by NS systematically inflates the number of genes acquired at the root of each MAL, and incorrectly assumes bacterial origins for these genes. A re-analysis of their data with appropriate phylogenetic models accounting for the dynamics of gene gain and loss between lineages supports the continuous acquisition of genes over long periods in the evolution of Archaea.

scholarly journals Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes

2019 ◽  
Vol 11 (10) ◽  
pp. 2750-2766 ◽  
Author(s):  
Gavin M Douglas ◽  
Morgan G I Langille
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
De Novo ◽  
Antibiotic Resistance Genes ◽  
Gene Families ◽  
Gene Gain ◽  
Loss Of Function ◽  
Shotgun Metagenomics ◽  
Gain And Loss ◽  
Natural Communities

Abstract High-throughput shotgun metagenomics sequencing has enabled the profiling of myriad natural communities. These data are commonly used to identify gene families and pathways that were potentially gained or lost in an environment and which may be involved in microbial adaptation. Despite the widespread interest in these events, there are no established best practices for identifying gene gain and loss in metagenomics data. Horizontal gene transfer (HGT) represents several mechanisms of gene gain that are especially of interest in clinical microbiology due to the rapid spread of antibiotic resistance genes in natural communities. Several additional mechanisms of gene gain and loss, including gene duplication, gene loss-of-function events, and de novo gene birth are also important to consider in the context of metagenomes but have been less studied. This review is largely focused on detecting HGT in prokaryotic metagenomes, but methods for detecting these other mechanisms are first discussed. For this article to be self-contained, we provide a general background on HGT and the different possible signatures of this process. Lastly, we discuss how improved assembly of genomes from metagenomes would be the most straight-forward approach for improving the inference of gene gain and loss events. Several recent technological advances could help improve metagenome assemblies: long-read sequencing, determining the physical proximity of contigs, optical mapping of short sequences along chromosomes, and single-cell metagenomics. The benefits and limitations of these advances are discussed and open questions in this area are highlighted.

scholarly journals Industrialization is associated with elevated rates of horizontal gene transfer in the human microbiome

2020 ◽  
Author(s):  
Mathieu Groussin ◽  
Mathilde Poyet ◽  
Ainara Sistiaga ◽  
Sean M. Kearney ◽  
Katya Moniz ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Close Contact ◽  
Human Microbiome ◽  
Antibiotic Resistance Genes ◽  
Human Populations ◽  
Bacterial Genomes ◽  
New Host ◽  
New Genes ◽  
Human Colonization

AbstractHorizontal Gene Transfer, the process by which bacteria acquire new genes and functions from non-parental sources, is common in the human microbiome 1,2. If the timescale of HGT is rapid compared to the timescale of human colonization, then it could have the effect of ‘personalizing’ bacterial genomes by providing incoming strains with the genes necessary to adapt to the diet or lifestyle of a new host. The extent to which HGT occurs on the timescale of human colonization, however, remains unclear. Here, we analyzed 6,188 newly isolated and sequenced gut bacteria from 34 individuals in 9 human populations, and show that HGT is more common among bacteria isolated from the same human host, indicating that the timescale of transfer is short compared to the timescale of human colonization. Comparing across 9 human populations reveals that high rates of transfer may be a recent development in human history linked to industrialization and urbanization. In addition, we find that the genes involved in transfer reflect the lifestyle of the human hosts, with elevated transfer of carbohydrate metabolism genes in hunter gatherer populations, and transfer of antibiotic resistance genes among pastoralists who live in close contact with livestock. These results suggest that host-associated bacterial genomes are not static within individuals, but continuously acquire new functionality based on host diet and lifestyle.

Sign in / Sign up

Export Citation Format

Share Document