Complete Genome Sequence of Pluralibacter gergoviae FB2, an N-Acyl Homoserine Lactone-Degrading Strain Isolated from Packed Fish Paste

Characterisation of the koala (Phascolarctos cinereus) pouch microbiota in a captive population reveals a dysbiotic compositional profile associated with neonatal mortality

BACKGROUND

Captive koala breeding programmes are essential for long-term species management. However, breeding efficacy is frequently impacted by high neonatal mortality rates in otherwise healthy females. Loss of pouch young typically occurs during early lactation without prior complications during parturition and is often attributed to bacterial infection. While these infections are thought to originate from the maternal pouch, little is known about the microbial composition of koala pouches. As such, we characterised the koala pouch microbiome across the reproductive cycle and identified bacteria associated with mortality in a cohort of 39 captive animals housed at two facilities.

RESULTS

Using 16S rRNA gene amplicon sequencing, we observed significant changes in pouch bacterial composition and diversity between reproductive time points, with the lowest diversity observed following parturition (Shannon entropy - 2.46). Of the 39 koalas initially sampled, 17 were successfully bred, after which seven animals lost pouch young (overall mortality rate - 41.18%). Compared to successful breeder pouches, which were largely dominated by Muribaculaceae (phylum - Bacteroidetes), unsuccessful breeder pouches exhibited persistent Enterobacteriaceae (phylum - Proteobacteria) dominance from early lactation until mortality occurred. We identified two species, Pluralibacter gergoviae and Klebsiella pneumoniae, which were associated with poor reproductive outcomes. In vitro antibiotic susceptibility testing identified resistance in both isolates to several antibiotics commonly used in koalas, with the former being multidrug resistant.

CONCLUSIONS

This study represents the first cultivation-independent characterisation of the koala pouch microbiota, and the first such investigation in marsupials associated with reproductive outcomes. Overall, our findings provide evidence that overgrowth of pathogenic organisms in the pouch during early development is associated with neonatal mortality in captive koalas. Our identification of previously unreported, multidrug resistant P. gergoviae strains linked to mortality also underscores the need for improved screening and monitoring procedures aimed at minimising neonatal mortality in future. Video Abstract.

Comparative genomic analyses of IncpA1763-KPC plasmids

Multi-replicon plasmids harboring the Inc_pA1763-KPC replicon together with other replicons are being increasingly reported among Enterobacteriaceae species. However, plasmids with single Inc_pA1763-KPC replicons are poorly studied as a different incompatibility (Inc) group, despite their rise in appearance in some strains. Inc_pA1763-KPC plasmids, pA1763-KPC, and p427113-2, from two clinical Klebsiella pneumoniae isolates were fully sequenced by high-throughput genome sequencing. Linear structural comparisons of Inc_pA1763-KPC backbone region were made between these two plasmids and six arbitrarily selected representative Inc_pA1763-KPC plasmids sequenced previously. A further detailed genomic comparison was carried out between plasmids pA1763-KPC, p427113-2, and pFB2.2, which show high homology across the backbone sequence to one another. Among all sequenced Inc_pA1763-KPC plasmids considered in this study, plasmids pA1763-KPC and p427113-2 showed the most complete Inc_pA1763-KPC backbones. These were composed of the Inc_pA1763-KPC replicon (repA_{IncpA1763-KPC} and its iterons), the 5.6-kb Inc_pA1763-KPC -type maintenance region, the 27.7-kb IncFII_K -type maintenance region, and the 36.6-kb IncFII_K -type conjugal transfer regions. Compared with pA1763-KPC or p427113-2, the backbone regions of the other analyzed Inc_pA1763-KPC plasmids had gradually undergone different deletions or truncations, but shared small and core Inc_pA1763-KPC backbones including the Inc_pA1763-KPC replicon, Inc_pA1763-KPC -type maintenance region, and residual IncFII_K -type maintenance region. Accessory modules integrated into Inc_pA1763-KPC backbones included the multidrug-resistant module bla_KPC-2 region in pA1763-KPC, the metal-resistance modules ars region together with ncr region in pFB2.2 and sil in pKPN-9a0d, the ISKpn14-to-IS26 region in p427113-2, and other non-resistance region in the respective plasmids. This detailed comparative genomics analysis of Inc_pA1763-KPC plasmids provides a deep insight into their diversification and evolution.

Storing of exoelectrogenic anolyte for efficient microbial fuel cell recovery

Starting up a microbial fuel cell (MFC) requires often a long-term culture enrichment period, which is a challenge after process upsets. The purpose of this study was to develop low-cost storage for MFC enrichment culture to enable prompt process recovery after upsets. Anolyte of an operating xylose-fed MFC was stored at different temperatures and for different time periods. Storing the anolyte for 1 week or 1 month at +4°C did not significantly affect power production, but the lag time for power production was increased from 2 days to 3 or 5 days, respectively. One month storing at -20°C increased the lag time to 7 days. The average power density in these MFCs varied between 1.2 and 1.7 W/m³. The share of dead cells (measured by live/dead staining) increased with storing time. After 6-month storage, the power production was insignificant. However, xylose removal remained similar in all cultures (99-100%) while volatile fatty acids production varied. The results indicate that fermentative organisms tolerated the long storage better than the exoelectrogens. As storing at +4°C is less energy intensive compared to freezing, anolyte storage at +4°C for a maximum of 1 month is recommended as start-up seed for MFC after process failure to enable efficient process recovery.