The animal gut as a melting pot for horizontal gene transfer

Shterzer, Naama; Mizrahi, Itzhak

doi:10.1139/cjm-2015-0049

Cited by 67 publications

(61 citation statements)

References 34 publications

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“…This relates to recurrent opportunities for the symbionts to reacquire genetic traits lost during host adaptation, thus avoiding host specialization. Replenishing genetic diversity through horizontal gene transfer with coinfecting symbionts and/or with environmental microorganisms during phases of host‐independent existence is likely relevant and common in this context, as suggested for other host‐associated microbes (Liu et al ., ; Shterzer and Mizrahi, ). Concordantly, the majority of Burkholderia strains described so far have large multireplicon genomes encoding diverse metabolic functions, rapid evolutionary rates and remarkable phenotypic diversity (Mahenthiralingam and Drevinek, ), which is in line with dynamic ecological interactions.…”

Section: Resultsmentioning

confidence: 98%

Symbiont dynamics and strain diversity in the defensive mutualism between Lagria beetles and Burkholderia

Flórez

Kaltenpoth

2017

Environmental Microbiology

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Defensive mutualisms are often facultative in nature, and their evolutionary dynamics can be shaped by changes in local antagonist communities or arms races with coevolving antagonists. Under these conditions, selection may favour hosts that flexibly acquire symbionts producing compounds with bioactivity against current antagonists. Here, we study the prevalence, dynamics and strain diversity of Burkholderia gladioli bacteria in Lagria beetles, a recently described protective symbiosis involving vertical transmission and antifungal defense for the host eggs. In Lagria hirta, we investigate the fate of the bacteria during the host life cycle. Despite a transmission route relying solely on the females, the bacteria are present in both sexes during the larval stage, suggesting a potentially multifaceted defensive role. In L. hirta and L. villosa adults, culture-dependent and -independent techniques revealed that individual beetles harbour diverse Burkholderia strains from at least two different phylogenetic clades, yet all closely related to free-living B. gladioli. Interestingly, rearing the beetles in the laboratory strongly impacted symbiont strain profiles in both beetle species. Our findings highlight the dynamic nature of the B. gladioli-Lagria symbiosis and present this as a valuable system for studying multiple strain coinfections, as well as the evolutionary and ecological factors regulating defensive symbiosis.

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Section: Resultsmentioning

confidence: 98%

Symbiont dynamics and strain diversity in the defensive mutualism between Lagria beetles and Burkholderia

Flórez

Kaltenpoth

2017

Environmental Microbiology

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“…Several species like Bacteroides thetaiotaomicron and Bacteroides ovatus harbor a large repertoire of genes for sensing, binding and metabolize carbohydrates4344, thus developing efficient strategies to harvest glycans. Our study emphasized a fibrolytic potential in B. uniformis and closely related yet undescribed strains.…”

Section: Discussionmentioning

confidence: 99%

A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic

Patrascu

Béguet-Crespel

Marinelli

et al. 2017

Sci Rep

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The digestion of dietary fibers is a major function of the human intestinal microbiota. So far this function has been attributed to the microorganisms inhabiting the colon, and many studies have focused on this distal part of the gastrointestinal tract using easily accessible fecal material. However, microbial fermentations, supported by the presence of short-chain fatty acids, are suspected to occur in the upper small intestine, particularly in the ileum. Using a fosmid library from the human ileal mucosa, we screened 20,000 clones for their activities against carboxymethylcellulose and xylans chosen as models of the major plant cell wall (PCW) polysaccharides from dietary fibres. Eleven positive clones revealed a broad range of CAZyme encoding genes from Bacteroides and Clostridiales species, as well as Polysaccharide Utilization Loci (PULs). The functional glycoside hydrolase genes were identified, and oligosaccharide break-down products examined from different polysaccharides including mixed-linkage β-glucans. CAZymes and PULs were also examined for their prevalence in human gut microbiome. Several clusters of genes of low prevalence in fecal microbiome suggested they belong to unidentified strains rather specifically established upstream the colon, in the ileum. Thus, the ileal mucosa-associated microbiota encompasses the enzymatic potential for PCW polysaccharide degradation in the small intestine.

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“…ARGs encoding defense mechanisms are readily transferred between pathogenic microorganisms through horizontal gene transfer (HGT) mediated by mobile genetic elements (MGEs), and integrons are considered to be the main contributors to the acquisition and spread of ARGs [14,15]. Shterzer and Mizrahi [16] have reported HGT occur in the gastrointestinal tracts of livestock, and it is enhanced in the presence of antibiotics [17,18]. In addition, both ARGs and heavy metal resistance genes (MRG) have similarly ancient origins [19].…”

Section: Introductionmentioning

confidence: 99%

Metagenomic analysis of effects of oxytetracycline and copper on antibiotic resistance genes and associated pathogenic hosts in swine manure compost

Guo

Wang

et al. 2020

Preprint

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Background: The proliferation of antibiotic resistance genes (ARGs) in compost and their horizontal transfer to human pathogenic bacteria (HPB) may lead to the failure of human antibiotics. However, the antibiotic resistome in compost has not been comprehensively characterized. This study used a metagenomic approach to obtain new insights into the effects of oxytetracycline (OTC) and copper (Cu) on the antibiotic resistome during swine manure composting and the risks posed to human health. Results: The results showed that composting reduced the abundances and diversity of ARGs and HPB in swine manure. In total, 289 ARG subtypes and 19 ARG types were detected in the samples with abundances ranging from 1.08 ´ 10 –1 to 9.39 ´ 10 –1 copies/16S rRNA, which mainly encoded tetracycline, aminoglycoside, and macrolide–lincosamide–streptogramin (MLS) resistance genes. The application of OTC and Cu, especially the combined application, exacerbated the compost resistome risk scores and specific ARG subtypes responded differently. Tetracycline, multidrug, and MLS resistance genes mainly affected resistance profiles of HPB throughout the composting process. HPB and intI1 had significant positive effects on determining the ARG profiles during the composting process, and the co-selective effect of heavy metals may increase the abundances of ARGs via strong positive effects on intI1 . In addition, the effect of mobile genetic elements on the horizontal gene transfer of ARGs should not be ignored. Conclusions: This study of the antibiotic resistome in compost indicates the need for effective regulation of the misuse of livestock and poultry feed additives in order to minimize the spread of the antibiotic resistome in agro-ecosystems and decrease the potential risk to public health. Keywords: Antibiotic resistome; Composting; Metagenome; Pathogenic host; Swine manure

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The animal gut as a melting pot for horizontal gene transfer

Cited by 67 publications

References 34 publications

Symbiont dynamics and strain diversity in the defensive mutualism between Lagria beetles and Burkholderia

Symbiont dynamics and strain diversity in the defensive mutualism between Lagria beetles and Burkholderia

A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic

Metagenomic analysis of effects of oxytetracycline and copper on antibiotic resistance genes and associated pathogenic hosts in swine manure compost

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