Phylogenomic analysis of the genus Delftia reveals distinct major lineages with ecological specializations

Bhat, Supriya V.; Maughan, Heather; Cameron, Andrew D. S.; Yost, Christopher K.

doi:10.1099/mgen.0.000864

“…Delftia spp. are broadly distributed in the environment and have agricultural relevance (Bhat et al 2022 ), the thriving growth of Delftia spp. on different amino acids provides strong evidence of their involvement in the transformation of amino acids within tobacco leaves (Juarez-Jimenez et al 2010 ).…”

Section: Resultsmentioning

confidence: 99%

The bacterial succession and its role in flavor compounds formation during the fermentation of cigar tobacco leaves

Si,

Zhou,

Zhao

et al. 2023

Bioresour. Bioprocess.

1

0

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Fermentation is the key process required for developing the characteristic properties of cigar tobacco leaves, complex microorganisms are involved in this process. However, the microbial fermentation mechanisms during the fermentation process have not been well-characterized. This study investigated the dynamic changes in conventional chemical composition, flavor compounds, and bacterial community during the fermentation of cigar tobacco leaves from Hainan and Sichuan provinces in China, as well as the potential roles of bacteria. Fermentation resulted in a reduction of conventional chemical components in tobacco leaves, with the exception of a noteworthy increase in insoluble protein content. Furthermore, the levels of 10 organic acids and 19 amino acids showed a significant decrease, whereas the concentration of 30 aromatic substances exhibited a unimodal trend. Before fermentation, the bacterial community structures and dominant bacteria in Hainan and Sichuan tobacco leaves differed significantly. As fermentation progressed, the community structures in the two regions became relatively similar, with Delftia, Ochrobactrum, Rhodococcus, and Stenotrophomonas being dominant. Furthermore, a total of 12 functional bacterial genera were identified in Hainan and Sichuan tobacco leaves using bidirectional orthogonal partial least squares (O2PLS) analysis. Delftia, Ochrobactrum, and Rhodococcus demonstrated a significant negative correlation with oleic acid and linoleic acid, while Stenotrophomonas and Delftia showed a significant negative correlation with undesirable amino acids, such as Ala and Glu. In addition, Bacillus showed a positive correlation with benzaldehyde, while Kocuria displayed a positive correlation with 2-acetylfuran, isophorone, 2, 6-nonadienal, and β-damascenone. The co-occurrence network analysis of microorganisms revealed a prevalence of positive correlations within the bacterial network, with non-abundant bacteria potentially contributing to the stabilization of the bacterial community. These findings can improve the overall tobacco quality and provide a novel perspective on the utilization of microorganisms in the fermentation of cigar tobacco leaves. Graphical Abstract

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“…The same was true for the characteristic bacterium Delftia in GZ, which had a significant positive correlation with pinoresinol diglucoside. Previous studies have shown that Delftia has a good application prospect in promoting plant growth and bioremediation (Bhat et al, 2022 ). Some of its members can be used to reduce the accumulation of Cd elements, agricultural inoculants, or bioremediation agents (Bhat et al, 2022 ; Lo et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

“…Previous studies have shown that Delftia has a good application prospect in promoting plant growth and bioremediation (Bhat et al, 2022 ). Some of its members can be used to reduce the accumulation of Cd elements, agricultural inoculants, or bioremediation agents (Bhat et al, 2022 ; Lo et al, 2022 ). In addition, there are other dominant endophytic bacteria including Thauera, Massilia , and Sphingomonas that have significant correlations with EC active ingredients.…”

Section: Discussionmentioning

confidence: 99%

Characteristics of endophytic bacteria and active ingredients in the Eucommiae cortex from different origins

Liang

¹

,

Zhou

²

,

Li

³

et al. 2023

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ObjectiveThis study aimed to explore the differences between Eucommiae cortex (EC) endophytic bacteria from different origins and their effects on the active ingredients of EC.MethodsA total of 10 samples of Eucommia ulmoides Oliv. (E. ulmoides) bark were collected from each of the following four regions, namely, Zunyi in Guizhou (GZ), Baokang in Hubei (HUB), Cili in Hunan (HUN), and Loyang in Shaanxi (SX). Subsequently, the contents of the main active ingredients of EC were determined by ultra-performance liquid chromatography (UPLC), and the endophytic bacteria of EC were detected by 16S rRNA sequencing. The relationship between the dominant endophytic bacteria and the active ingredients was investigated by correlation analysis.ResultsA total of 4,551 different operational taxonomic units (OTUs) were delineated in the four groups of samples, of which 585, 439, 957, and 684 genera were annotated from GZ, HUB, HUN, and SX, respectively. The richness and diversity of endophytic bacteria from different origins were ranked as HUN > SX > GZ or HUB. The analysis demonstrated that there was no significant correlation between the diversity and richness of endophytic bacteria in EC and its active ingredients. Nevertheless, notable variations in the community structures of endophytic bacteria were observed across different origins, and they had a considerable impact on certain active ingredients in EC. Comamonas and Cedecea were the dominant genera. Characteristic bacteria of different origins could be clearly distinguished. Simultaneous, significant correlations had been identified between some characteristic endophytic bacteria derived from different origins and active ingredients of EC. For example, Delftia, a characteristic bacterium from GZ, showed a significant positive correlation with pinoresinol diglucoside. Paenibacillus and Klebsiella, two characteristic bacteria from HUB, exhibited significant positive correlations with geniposidic acid. Thauera, a characteristic bacterium from HUN, demonstrated a significant positive correlation with geniposide. Brevundimonas, a characteristic bacterium from SX, displayed a significant positive correlation with pinoresinol diglucoside.ConclusionThere was a complex correlation between EC endophytic bacteria and active ingredient content, while EC endophytic bacteria from different origins had significant differences at the genus level.

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“…Several are environmental bacteria that can also act as opportunistic pathogens (Micrococcus, Stutzerimonas, Exiguobacterium, Corynebacterium, Ralstonia, Achromobacter, Acinetobacter), while a few others have industrial relevance, including in enzyme production (Delftia, Exiguobacterium) [46].…”

Section: Discussionmentioning

confidence: 99%

“…Some of these genera are at the same time typical representatives of the normal human microbiome, mostly associated with the skin/mucosa or gut, or pathogens (such as Cutibacterium , Escherichia , Staphylococcus , Pseudomonas , Malassezia , Streptococcus ). Several are environmental bacteria that can also act as opportunistic pathogens ( Micrococcus , Stutzerimonas , Exiguobacterium , Corynebacterium , Ralstonia , Achromobacter , Acinetobacter ), while a few others have industrial relevance, including in enzyme production ( Delftia , Exiguobacterium ) [46].…”

Section: Discussionmentioning

confidence: 99%

Metatranscriptome analysis of blood in healthy individuals and irritable bowel syndrome patients

Jagare,

Rozenberga,

Silamikelis

et al. 2023

Journal of Medical Microbiology

2

0

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Introduction. Although the presence of micro-organisms in the blood of healthy humans is a relatively new concept, there is a growing amount of evidence that blood might have its own microbiome. Gap Statement. Previous research has targeted the taxonomic composition of the blood microbiome using DNA-based sequencing methods, while little information is known about the presence of microbial transcripts obtained from the blood and their relation to conditions connected with increased gut permeability. Aim. To detect potentially alive and active micro-organisms and investigate differences in taxonomic composition between healthy people and patients with irritable bowel syndrome (IBS), we used the metatranscriptomics approach. Methodology. We collected blood samples from 23 IBS patients and 26 volunteers from the general population, and performed RNAseq on the isolated RNA. Reads corresponding to microbial genomes were identified with Kraken 2’s standard plus protozoa and fungi database, and re-estimated at genus level with Bracken 2.7. We looked for trends in the taxonomic composition, making a comparison between the IBS and control groups, accounting for other different factors. Results. The dominant genera in the blood microbiome were found to be Cutibacterium , Bradyrhizobium , Escherichia , Pseudomonas , Micrococcus , Delftia , Mediterraneibacter , Staphylococcus , Stutzerimonas and Ralstonia . Some of these are typical environmental bacteria and could partially represent contamination. However, analysis of sequences from the negative controls suggested that some genera which are characteristic of the gut microbiome ( Mediterraneibacter , Blautia , Collinsella , Klebsiella , Coprococcus , Dysosmobacter , Anaerostipes , Faecalibacterium , Dorea , Simiaoa , Bifidobacterium , Alistipes, Prevotella, Ruminococcus ) are less likely to be a result of contamination. Differential analysis of microbes between groups showed that some taxa associated with the gut microbiome ( Blautia , Faecalibacterium , Dorea , Bifidobacterium , Clostridium , Christensenella ) are more prevalent in IBS patients compared to the general population. No significant correlations with any other factors were identified. Conclusion. Our findings support the existence of the blood microbiome and suggest the gut and possibly the oral microbiome as its origin, while the skin microbiome is a possible but less certain source. The blood microbiome is likely influenced by states of increased gut permeability such as IBS.

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Phylogenomic analysis of the genus Delftia reveals distinct major lineages with ecological specializations

Cited by 9 publications

References 54 publications

The bacterial succession and its role in flavor compounds formation during the fermentation of cigar tobacco leaves

The bacterial succession and its role in flavor compounds formation during the fermentation of cigar tobacco leaves

Characteristics of endophytic bacteria and active ingredients in the Eucommiae cortex from different origins

Metatranscriptome analysis of blood in healthy individuals and irritable bowel syndrome patients

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