Gracilibacillus suaedae sp. nov., an indole acetic acid-producing endophyte isolated from a root of Suaeda salsa

Intestinal microbiota and metabolome perturbations in ischemic and idiopathic dilated cardiomyopathy

BACKGROUND

Various clinical similarities are present in ischemic (ICM) and idiopathic dilated cardiomyopathy (IDCM), leading to ambiguity on some occasions. Previous studies have reported that intestinal microbiota appeared dysbiosis in ICM, whether implicating in the IDCM remains unclear. The aim of this study was to assess the alterations in intestinal microbiota and fecal metabolites in ICM and IDCM.

METHODS

ICM (n = 20), IDCM (n = 22), and healthy controls (HC, n = 20) were enrolled in this study. Stool samples were collected for 16S rRNA gene sequencing and gas chromatography-mass spectrometry (GC-MS) analysis.

RESULTS

Both ICM and IDCM exhibited reduced alpha diversity and altered microbial community structure compared to HC. At the genus level, nine taxa including Blautia, [Ruminococcus]_torques_group, Christensenellaceae_R-7_group, UCG-002, Corynebacterium, Oceanobacillus, Gracilibacillus, Klebsiella and Citrobacter was specific to ICM, whereas one taxa Alistipes uniquely altered in IDCM. Likewise, these changes were accompanied by significant metabolic differences. Further differential analysis displayed that 18 and 14 specific metabolites uniquely changed in ICM and IDCM, respectively. The heatmap was generated to display the association between genera and metabolites. Receiver operating characteristic curve (ROC) analysis confirmed the predictive value of the distinct microbial-metabolite features in disease status. The results showed that microbial (area under curve, AUC = 0.95) and metabolic signatures (AUC = 0.84) were effective in discriminating ICM from HC. Based on the specific microbial and metabolic features, the patients with IDCM could be separated from HC with an AUC of 0.80 and 0.87, respectively. Furthermore, the gut microbial genus (AUC = 0.88) and metabolite model (AUC = 0.89) were comparable in predicting IDCM from ICM. Especially, the combination of fecal microbial-metabolic features improved the ability to differentiate IDCM from ICM with an AUC of 0.96.

CONCLUSION

Our findings highlighted the alterations of gut microbiota and metabolites in different types of cardiomyopathies, providing insights into the pathophysiological mechanisms of myocardial diseases. Moreover, multi-omics analysis of fecal samples holds promise as a non-invasive tool for distinguishing disease status.

Gracilibacillus salinarum sp. nov. and Gracilibacillus caseinilyticus sp. nov., halotolerant bacteria isolated from a saltern environment

Two aerobic, Gram-stain-positive, spore-forming motile bacterial strains, designated SSPM10-3T and SSWR10-1T, were isolated from salterns in Jeollanam province of South Korea. Both strains were halotolerant and grew well in 5 % NaCl but not in 20 and 25% NaCl, respectively. Optimal growth was observed with 5 % NaCl, at 30 °C and at pH 7.0-8.0. On the basis of the results of phylogenetic analysis using 16S rRNA gene sequence, both the strains were placed within the genus Gracilibacillus with Gracilibacillus massiliensis (98.65 % similarity) as their nearest neighbour. Menaquinone-7 (MK-7) (97 %) was the major isoprenoid quinone in both strains and major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. Orthologous average nucleotide identity with usearch (OrthoANIu) and digital DNA-DNA hybridisation (dDDH) percentage comparison indicated that SSPM10-3T and SSWR10-1T exhibited highest similarity with G. massiliensis Awa-1T at 74.27 % and 21.0 and 74.23 % and 20.0 %, respectively. The DNA G+C contents of the strains were 39.1 % (SSPM10-3T) and 38.5 % (SSWR10-1T). Members of the genus Gracilibacillus, both strains were distinct from each other with respect to their ability to produce urease, β-glucosidase, assimilation of inulin and methyl-α-d-glucopyranoside and degradation of casein. Compared with each other, ANI and d4 dDDH calculations were only 88.2 % and 36.3 %, well below the cut-off values for species delineation for each index. On the basis of their phenotypic, physiological, biochemical and phylogenetic characteristics,SSPM10-3T and SSWR10-1T represent distinct novel species for which names Gracilibacillus salinarum SSPM10-3T and Gracilibacillus caseinilyticus SSWR10-1T are proposed. The type strains are SSPM10-3T (=KACC 21933T =NBRC 115502T) and SSWR10-1T (=KACC 21934T =NBRC 115503T).

Acuticoccus kalidii sp. nov., a 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing endophyte from a root of Kalidium cuspidatum

A 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing, Gram-stain-negative, strictly aerobic, non-motile, yellow-reddish, oval-shaped bacterial strain, designated M5D2P5^T, was isolated from a root of Kalidium cuspidatum, in Tumd Right Banner, Inner Mongolia, PR China. M5D2P5^T grew at 10-40 °C (optimum 30-35 °C), pH 5.0-10.0 (optimum pH 8.0) and with 0-7% NaCl (optimum 3.0 %). The strain was positive for catalase and oxidase. The phylogenetic trees based on 16S rRNA gene sequences indicated that M5D2P5^T clustered with Acuticoccus yangtzensis JL1095^T, and shared 98.0, 97.3, 97.2, 96.9 and less than 96.9 % 16S rRNA gene similarities to A. yangtzensis JL1095^T, Acuticoccus mangrovi B2012^T, Acuticoccus sediminis PTG4-2^T, Acuticoccus kandeliae J103^T, and all the other type strains, respectively. However, the phylogenomic tree showed it clustered with A. kandeliae J103^T. M5D2P5^T contained Q-10 as the major respiratory quinone, as well as two minor respiratory quinones, Q-7 and Q-8. Its major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified glycolipid, and four unidentified lipids. The genomic DNA G+C content was 66.5 %. The digital DNA-DNA hybridization score and the average nucleotide identity based on blast values of M5D2P5^T to A. yangtzensis JL1095^T, A. kandeliae J103^T, A. mangrovi B2012^T, and A. sediminis PTG4-2^T, were 20.8, 23.7, 20.7, and 21.5 %, and 73.3, 79.5, 74.4, and 73.7 %, respectively. The phylogenetic and phenotypic characteristics allowed the discrimination of M5D2P5^T from its phylogenetic relatives. The novel species Acuticoccus kalidii sp. nov. is therefore proposed, and the type strain is M5D2P5^T (=CGMCC 1.19149^T=KCTC 92132^T).

Corynebacterium kalidii sp. nov, an endophyte from a shoot of the halophyte Kalidium cuspidatum

A Gram-stain-positive, non-motile, rod-shaped bacterial strain designated LD5P10^T was isolated from a root of Kalidium cuspidatum, in Tumd Right Banner, Inner Mongolia, China. The strain grew at 4-40 ℃ (optimum 30 ℃), and pH 5.0-10.0 (optimum pH 8.0), and in the presence of 0-16.0% (w/v) NaCl (optimum 2.0%). The strain was positive for catalase, and urease, and negative for nitrate reduction, and oxidase. The phylogenetic trees based on the 16S rRNA gene sequences and the whole genome sequence both revealed that strain LD5P10^T clustered tightly with Corynebacterium glyciniphilum AJ 3170^T and shared 98.1, 98.1, and < 98.1% of the 16S rRNA gene sequence similarities with strains C. glyciniphilum AJ 3170^T, C. variabile DSM 20132^T, and all the other current type strains. Strain LD5P10^T contained MK-9 as the major respiratory quinone. Its major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphoglycolipid, two unidentified lipids, and two unidentified phospholipids. Its major fatty acids were C_16:0 and C_18:1 ω9c. The genomic DNA G + C content was 69.0%. The average nucleotide identity based on BLAST (ANIb), amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values of strain LD5P10^T to C. glyciniphilum AJ 3170^T and C. variabile DSM 20132^T were 82.9 and 76.4%, 85.3 and 69.4%, and 25.8 and 20.9%, respectively. The phylogenetic, physiological, and phenotypic results allowed the discrimination of strain LD5P10^T from its phylogenetic relatives. Corynebacterium kalidii sp. nov. is, therefore, proposed with strain LD5P10^T (= CGMCC 1.19144^T = JCM 35048^T) as the type strain.