Construction of genetically marked Ruminococcus albus strains and conjugal transfer of plasmid pAMβ1 into them

Establishing genetic manipulation for novel strains of human gut bacteria

Recent years have seen the development of high-accuracy and high-throughput genetic manipulation techniques, which have greatly improved our understanding of genetically tractable microbes. However, challenges remain in establishing genetic manipulation techniques in novel organisms, owing largely to exogenous DNA defence mechanisms, lack of selectable markers, lack of efficient methods to introduce exogenous DNA and an inability of genetic vectors to replicate in their new host. In this review, we describe some of the techniques that are available for genetic manipulation of novel microorganisms. While many reviews exist that focus on the final step in genetic manipulation, the editing of recipient DNA, we particularly focus on the first step in this process, the transfer of exogenous DNA into a strain of interest. Examples illustrating the use of these techniques are provided for a selection of human gut bacteria in which genetic tractability has been established, such as Bifidobacterium, Bacteroides and Roseburia. Ultimately, this review aims to provide an information source for researchers interested in developing genetic manipulation techniques for novel bacterial strains, particularly those of the human gut microbiota.

The Ruminococci: key symbionts of the gut ecosystem

Mammalian gut microbial communities form intricate mutualisms with their hosts, which have profound implications on overall health. One group of important gut microbial mutualists are bacteria in the genus Ruminococcus, which serve to degrade and convert complex polysaccharides into a variety of nutrients for their hosts. Isolated decades ago from the bovine rumen, ruminococci have since been cultured from other ruminant and non-ruminant sources, and next-generation sequencing has further shown their distribution to be widespread in a diversity of animal hosts. While most ruminococci that have been studied are those capable of degrading cellulose, much less is known about non-cellulolytic, nonruminant-associated species, such as those found in humans. Furthermore, a mechanistic understanding of the role of Ruminococcus spp. in their respective hosts is still a work in progress. This review highlights the broad work done on species within the genus Ruminococcus with respect to their physiology, phylogenetic relatedness, and their potential impact on host health.

Meta-analysis of experimental data concerning antimicrobial resistance gene transfer rates during conjugation

This paper presents the results of a meta-analysis of published transfer rates of antimicrobial resistance genes. A total of 34 papers were identified, of which 28 contained rates estimated in relation to either donor or recipient bacterial counts. The published rates ranged from 10(-2) to 10(-9). Generalized linear modeling was conducted to identify the factors influencing this variation. Highly significant associations between transfer frequency and both the donor (P = 1.2 x 10(-4)) and recipient (P = 1.0 x 10(-5)) genera were found. Also significant was whether the donor and recipient strains were of the same genus (P = 0.023) and the nature of the genetic element (P = 0.0019). The type of experiment, in vivo or in vitro, approached statistical significance (P = 0.12). Parameter estimates from a general linear model were used to estimate the probability of transfer of antimicrobial resistance genes to potential pathogens in the intestine following oral ingestion. The mean logarithms of these probabilities are in the range of [-7.0, -3.1]. These probability distributions are suitable for use in the quantitative assessment of the risk of transfer of antimicrobial resistance genes to the intestinal flora of humans and animals.

Structural analysis of a new cryptic plasmid pAR67 isolated from Ruminococcus albus AR67

The complete nucleotide sequence of a new cryptic plasmid pAR67 isolated from a rumen bacterium Ruminococcus albus AR67 has been determined. The plasmid pAR67 was 3419 bp in size with a 45% GC content. Two open reading frames, ORF1 and ORF2, encoding potential polypeptides of 285 and 165 amino acids, with limited sequence similarity to replication and mobilization proteins, respectively, were identified within the sequence. The region upstream of ORF1 had an AT-rich (80%) segment followed by four 19-bp direct repeats, which is similar to the structural organization characteristic of replication origins of some bacterial plasmids.

Complete nucleotide sequence of a cryptic plasmid, pBAW301, from the ruminal anaerobe Ruminococcus flavefaciens R13e2

The complete nucleotide sequence of a cryptic plasmid designated pBAW301, from the Gram-positive ruminal bacterium Ruminococcus flavefaciens R13e2, has been determined. This plasmid is 1768 bp in size and has an overall G+C content of 43.5%. Computer analysis of the sequence data revealed an open reading frame, ORF1 (256 amino acids), which is similar to the Rep protein of the Bacillus borstelensis plasmid pHT926. ORF1 is preceded by Shine-Dalgarno and Escherichia coli-10 and -35 like sequences. Nine smaller open reading frames showed no significant homologies to known protein sequences. Analysis of replication intermediates and the nucleotide sequence indicate that the plasmid does not replicate by a rolling-circle mode of replication similar to other plasmids from Gram-positive bacteria. Moreover, sequences typical of theta replication origins were not found in the nucleotide sequence of pBAW301. These data suggest that this plasmid either replicates by an as yet undescribed mechanism, or represents a new class of theta replicating plasmids.

Enumeration of transconjugated Ruminococcus albus and its survival in the goat rumen microcosm

A transconjugant Ruminococcus albus A3 culture was released into a goat rumen, and the extent of its survival in the rumen microcosm was measured by distinguishing this bacterium from indigenous microbes by antibiotic resistance. A3 cells remained roughly constant for 14 days in this goat rumen.