Paenibacillus albicereus sp. nov. and Niallia alba sp. nov., isolated from digestive syrup

Ethanol-Producing Enterocloster bolteae Is Enriched in Chronic Hepatitis B-Associated Gut Dysbiosis: A Case-Control Culturomics Study

BACKGROUND

Hepatitis B virus (HBV) infection is a global health epidemic that causes fatal complications, leading to liver cirrhosis and hepatocellular carcinoma. The link between HBV-related dysbiosis and specific bacterial taxa is still under investigation. Enterocloster is emerging as a new genus (formerly Clostridium), including Enterocloster bolteae, a gut pathogen previously associated with dysbiosis and human diseases such as autism, multiple sclerosis, and inflammatory bowel diseases. Its role in liver diseases, especially HBV infection, is not reported.

METHODS

The fecal samples of eight patients with chronic HBV infection and ten healthy individuals were analyzed using the high-throughput culturomics approach and compared to 16S rRNA sequencing. Quantification of ethanol, known for its damaging effect on the liver, produced from bacterial strains enriched in chronic HBV was carried out by gas chromatography-mass spectrometry.

RESULTS

Using culturomics, 29,120 isolated colonies were analyzed by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-TOF); 340 species were identified (240 species in chronic HBV samples, 254 species in control samples) belonging to 169 genera and 6 phyla. In the chronic HBV group, 65 species were already known in the literature; 48 were associated with humans but had not been previously found in the gut, and 17 had never been associated with humans previously. Six species were newly isolated in our study. By comparing bacterial species frequency, three bacterial genera were serendipitously found with significantly enriched bacterial diversity in patients with chronic HBV: Enterocloster, Clostridium, and Streptococcus (p = 0.0016, p = 0.041, p = 0.053, respectively). However, metagenomics could not identify this enrichment, possibly concerning its insufficient taxonomical resolution (equivocal assignment of operational taxonomic units). At the species level, the significantly enriched species in the chronic HBV group almost all belonged to class Clostridia, such as Clostridium perfringens, Clostridium sporogenes, Enterocloster aldenensis, Enterocloster bolteae, Enterocloster clostridioformis, and Clostridium innocuum. Two E. bolteae strains, isolated from two patients with chronic HBV infection, showed high ethanol production (27 and 200 mM).

CONCLUSIONS

Culturomics allowed us to identify Enterocloster species, specifically, E. bolteae, enriched in the gut microbiota of patients with chronic HBV. These species had never been isolated in chronic HBV infection before. Moreover, ethanol production by E. bolteae strains isolated from the chronic HBV group could contribute to liver disease progression. Additionally, culturomics might be critical for better elucidating the relationship between dysbiosis and chronic HBV infection in the future.

Paenibacillus sabuli sp. nov., isolated from the South China Sea

A Gram-positive, rod-shaped, motile, spore-forming bacterium, designated strain IB182496T, was isolated from coastal sand of the South China Sea. The strain grew optimally at pH 7.0–9.0, 20–30 °C, and with NaCl 3.0–5.0 %. The predominant menaquinone was MK-7 and the major cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. The polar lipids in the cell wall included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids and one unidentified lipid. The comparison of 16S rRNA gene sequences indicated that strain IB182496T was most closely related to ‘Paenibacillus sambharensis’ SMB1 and Paenibacillus tarimensis SA-7-6T with similarities of 95.7 and 95.5 %, respectively. The whole-genome average nucleotide identity values between strain IB182496T and the two reference strains were 70.8 and 70.5%, and the digital DNA–DNA hybridization values were 18.7 and 18.0 %, respectively. Genomic analyses showed that strain IB182496T presented a genome of 6.22 Mbp with chromosomal G+C content of 60.3 %, and a total of 5261 genes were predicted. The combined phylogenetic relatedness, phenotypic and genotypic features supported the conclusion that strain IB182496T should be considered as representing a novel species of the genus Paenibacillus , for which we propose the name Paenibacillus sabuli sp. nov. with the type strain IB182496T (=MCCC 1K04627T=JCM 34216T).