Parabacteroides distasonis:intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health

Parabacteroides distasonis is the type strain for the genus Parabacteroides, a group of gram-negative anaerobic bacteria that commonly colonize the gastrointestinal tract of numerous species. First isolated in the 1930s from a clinical specimen as Bacteroides distasonis, the strain was re-classified to form the new genus Parabacteroides in 2006. Currently, the genus consists of 15 species, 10 of which are listed as 'validly named' (P. acidifaciens, P. chartae, P. chinchillae, P. chongii, P. distasonis, P. faecis, P. goldsteinii, P. gordonii, P. johnsonii, and P. merdae) and 5 'not validly named' (P. bouchesdurhonensis, P. massiliensis, P. pacaensis, P. provencensis, and P. timonensis) by the List of Prokaryotic names with Standing in Nomenclature. The Parabacteroides genus has been associated with reports of both beneficial and pathogenic effects in human health. Herein, we review the literature on the history, ecology, diseases, antimicrobial resistance, and genetics of this bacterium, illustrating the effects of P. distasonis on human and animal health

Artificial Polyploidy Improves Bacterial Single Cell Genome Recovery

BACKGROUND: Single cell genomics (SCG) is a combination of methods whose goal is to decipher the complete genomic sequence from a single cell and has been applied mostly to organisms with smaller genomes, such as bacteria and archaea. Prior single cell studies showed that a significant portion of a genome could be obtained. However, breakages of genomic DNA and amplification bias have made it very challenging to acquire a complete genome with single cells. We investigated an artificial method to induce polyploidy in Bacillus subtilis ATCC 6633 by blocking cell division and have shown that we can significantly improve the performance of genomic sequencing from a single cell. METHODOLOGY/PRINCIPAL FINDINGS: We inhibited the bacterial cytoskeleton protein FtsZ in B.subtilis with an FtsZ-inhibiting compound, PC190723, resulting in larger undivided single cells with multiple copies of its genome. qPCR assays of these larger, sorted cells showed higher DNA content, have less amplification bias, and greater genomic recovery than untreated cells. SIGNIFICANCE: The method presented here shows the potential to obtain a nearly complete genome sequence from a single bacterial cell. With millions of uncultured bacterial species in nature, this method holds tremendous promise to provide insight into the genomic novelty of yet-to-be discovered species, and given the temporary effects of artificial polyploidy coupled with the ability to sort and distinguish differences in cell size and genomic DNA content, may allow recovery of specific organisms in addition to their genomes

Draft genome sequence of Thauera sp. strain SWB20, isolated from a Singapore wastewater treatment facility using gel microdroplets

We report here the genome sequence of Thauera sp. strain SWB20, isolated from a Singaporean wastewater treatment facility using gel microdroplets (GMDs) and single-cell genomics (SCG). This approach provided a single clonal microcolony that was sufficient to obtain a 4.9-Mbp genome assembly of an ecologically relevant Thauera species.Published versio

<i>B. subtilis</i> response to PC190723 treatment: Increased DNA content.

<p>DNA content was assessed for PC190723 treated (maximum effect from ten replicates) and control cells via six replicates of 50 sorted cells for primer sets A (located near the origin) and B (located near the terminus). Theta or multi-fork replication may account for the discrepant reports from both primer sets. Cells treated for 50 minutes had more DNA content than the respective untreated controls. Prolonged drug exposure may account for the reducing DNA content at 60-min treatment as related to DNA degradation. Error bars are 95% CI.</p

PC190723-treated cells have increased genomic coverage and less amplification bias.

<p>(<i>A</i>) Genome coverage of mapped reads increases with treatment. Also, LBS correlates with genome coverage (R² = 0.6998, p = 0.1634). Best-fit line determined by least-squares linear regression. (<i>B</i>) Mapped to <i>B. subtilis</i> ATCC 6633 genome, untreated control cells have more gaps (red lines) than inhibited cells. Similar gap placement on the genome suggests amplification bias. Because of increased genomic template in polyploid cells, the number of gaps is greatly reduced (black circles).</p

<i>B. subtilis</i> response to PC190723 treatment: Increased cell size.

<p>(<i>A</i>) Typical cytographs from treatments illustrate increase in cell size in PC190723-treated <i>B. subtilis</i> versus untreated control and DMSO-treated cells at 60 minutes after treatment. Crosshairs were made at the mode of the untreated control population and applied to the DMSO- and PC190723-treated cytographs. Resultant quadrants give the relative percentage of the population (from 100,000 cells) inhabiting each quadrant. Thus, in quadrant two (Q2) of the control population, 44.7% of the cells are observed, while over 80% are observed in the PC190723-treated population. DMSO has no effect on cell size. Percentages are calculated by omitting the lower left population (<i>A</i> Control: black circle) from each cytograph, which likely contains dead cells and cell debris. (<i>B</i>) By determining ΔQ2 over time, cell size is shown to plateau after 60 minutes. Error bars are 95% CI. (<i>C</i>) Typical light microscope images of sorted untreated control and PC190723-treated cells. PC190723-treated cells are longer than untreated control cells, but the diameter appears unchanged.</p

Summary of candidates selected for sequencing.

a<p>normalized to nearly 8.78×10⁶ raw reads.</p>b<p>normalized to 1.0×10⁷ raw reads.</p