Comparative genomic analysis of hyper-ammonia producing Acetoanaerobium sticklandii DSM 519 with purinolytic Gottschalkia acidurici 9a and pathogenic Peptoclostridium difficile 630

Effect of propionate-cultured sludge augmentation on methane production from upflow anaerobic sludge blanket systems treating fresh landfill leachate

This research investigates the effect of propionate-cultured sludge augmentation on methane (CH₄) production from upflow anaerobic sludge blanket systems (UASB) treating fresh landfill leachate. In the study, both UASB reactors (UASB 1 and UASB 2) contained acclimatized seed sludge, and UASB 2 was augmented with propionate-cultured sludge. The organic loading rate (OLR) was varied between 120.6, 84.4, 48.2, and 12.0 gCOD/L·d. The experimental results indicated that the optimal OLR of UASB 1 (non-augmentation) was 48.2 gCOD/L·d, achieving the CH₄ production of 4019 mL/d. Meanwhile, the optimal OLR of UASB 2 was 12.0 gCOD/L·d, achieving the CH₄ yield of 6299 mL/d. The dominant bacterial community in the propionate-cultured sludge included the genera Methanothrix, Methanosaeta, Methanoculleus, Syntrophobacter, Smithella, Pelotomamulum, which are the VFA-degrading bacteria and methanogens responsible for unblocking the CH₄ pathway bottleneck. Essentially, the novelty of this research lies in the use of propionate-cultured sludge to augment the UASB reactor in order to enhance CH₄ production from fresh landfill leachate.

Discovery of novel virulence mechanisms in Clostridium botulinum type A3 using genome-wide analysis

OBJECTIVE

Clostridium botulinum type A is a neurotoxin-producing, spore-forming anaerobic bacterium that causes botulism in humans. The evolutionary genomic context of this organism is not yet known to understand its molecular virulence mechanisms in the human intestinal tract. Hence, this study aimed to investigate the mechanisms underlying virulence and pathogenesis by comparing the genomic contexts across species, serotypes, and subtypes.

METHODS

A comparative genomic approach was used to analyze evolutionary genomic relationships, intergenomic distances, syntenic blocks, replication origins, and gene abundance with phylogenomic neighbors.

RESULTS

Type A strains have shown genomic proximity to group I strains with distinct accessory genes and vary even within subtypes. Phylogenomic data showed that type C and D strains were distantly related to a group I and group II strains. Synthetic plots indicated that orthologous genes might have evolved from Clostridial ancestry to subtype A3 strains, whereas syntonic out-paralogs might have emerged between subtypes A3 and A1 through α-events. Gene abundance analysis revealed the key roles of genes involved in biofilm formation, cell-cell communication, human diseases, and drug resistance compared to the pathogenic Clostridia. Moreover, we identified 43 unique genes in the type A3 genome, of which 29 were involved in the pathophysiological processes and other genes contributed to amino acid metabolism. The C. botulinum type A3 genome contains 14 new virulence proteins that can provide the ability to confer antibiotic resistance, virulence exertion and adherence to host cells, the host immune system, and mobility of extrachromosomal genetic elements.

CONCLUSION

The results of our study provide insight into the understanding of new virulence mechanisms to discover new therapeutics for the treatment of human diseases caused by type A3 strains.

Feedstock-dependent abundance of functional genes related to nitrogen transformation controlled nitrogen loss in composting

The objective of this work was to explore how selection of feedstock affects nitrogen cycle genes during composting, which eventually determines the nitrogen loss. Four composting mixes (CM: chicken manure; SM: sheep manure; MM_1/3: mixed manure with CM: SM = 1:3 w/w, MM_3/1: CM: SM = 3:1 w/w) were investigated. Results showed that adding 25 % and 75 % SM to CM reduced 26.5 % and 57.9 % nitrogen loss, respectively. CM contained more ammonification genes and nrfA gene, while SM had more denitrification genes. Nitrogen fixation genes in CM were slightly higher than that in SM at the initial stage, but they sharply dropped off as the composting entered the high temperature stage. MM_1/3 showed significantly reduced ammonification genes than CM, and increased nitrogen fixation and NH₄⁺ assimilation genes. Therefore, adding SM to CM could change the abundance of genes and enzymes related to nitrogen cycle to reduce nitrogen loss.

Sodium butyrate reduces ammonia production in the cecum of laying hens by regulating ammonia-producing bacteria

Sodium butyrate is a commonly used feed additive and can reduce ammonia (NH₃) emissions from laying hens, but the mechanism of this effect is unknown. In this study, the sodium butyrate and cecal content of Lohmann pink laying hens were measured, and in vitro fermentation experiments and NH₃-producing bacteria coculture experiments were carried out to explore the relationship between NH₃ emissions and its associated microbiota metabolism. Sodium butyrate was found to significantly reduce NH₃ emission from the cecal microbial fermentation of Lohmann pink laying hens (P < 0.05). The concentration of NO₃^--N in the fermentation broth of the sodium butyrate-supplemented group increased significantly, and the concentration of NH₄⁺-N decreased significantly (P < 0.05). Moreover, sodium butyrate significantly reduced the abundance of harmful bacteria and increased the abundance of beneficial bacteria in the cecum. The culturable NH₃-producing bacteria consisted mainly of Escherichia and Shigella, such as Escherichia fergusonii, Escherichia marmotae and Shigella flexnerii. Among them, E. fergusonii had the highest potential for NH₃ production. The coculture experiment showed that sodium butyrate can significantly downregulate the expression of the lpdA, sdaA, gcvP, gcvH and gcvT genes of E. fergusonii (P < 0.05), thus reducing the NH₃ emission produced by the bacteria during metabolism. In general, sodium butyrate regulated NH₃-producing bacteria to reduce NH₃ production in the cecum of laying hens. These results are of great significance for NH₃ emission reduction in the layer breeding industry and for future research.