|
1
|
Peng M, Lin W, Zhou A, Jiang Z, Zhou F, Wang Z. High genetic diversity and different type VI secretion systems in Enterobacter species revealed by comparative genomics analysis. BMC Microbiol 2024; 24:26. [PMID: 38238664 PMCID: PMC10797944 DOI: 10.1186/s12866-023-03164-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/18/2023] [Indexed: 01/22/2024] Open
Abstract
The human-pathogenic Enterobacter species are widely distributed in diverse environmental conditions, however, the understanding of the virulence factors and genetic variations within the genus is very limited. In this study, we performed comparative genomics analysis of 49 strains originated from diverse niches and belonged to eight Enterobacter species, in order to further understand the mechanism of adaption to the environment in Enterobacter. The results showed that they had an open pan-genome and high genomic diversity which allowed adaptation to distinctive ecological niches. We found the number of secretion systems was the highest among various virulence factors in these Enterobacter strains. Three types of T6SS gene clusters including T6SS-A, T6SS-B and T6SS-C were detected in most Enterobacter strains. T6SS-A and T6SS-B shared 13 specific core genes, but they had different gene structures, suggesting they probably have different biological functions. Notably, T6SS-C was restricted to E. cancerogenus. We detected a T6SS gene cluster, highly similar to T6SS-C (91.2%), in the remote related Citrobacter rodenitum, suggesting that this unique gene cluster was probably acquired by horizontal gene transfer. The genomes of Enterobacter strains possess high genetic diversity, limited number of conserved core genes, and multiple copies of T6SS gene clusters with differentiated structures, suggesting that the origins of T6SS were not by duplication instead by independent acquisition. These findings provide valuable information for better understanding of the functional features of Enterobacter species and their evolutionary relationships.
Collapse
Affiliation(s)
- Mu Peng
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, China.
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China.
| | - Weiyuan Lin
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China
| | - Aifen Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Zhihui Jiang
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China
| | - Fangzhen Zhou
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China
| | - Zhiyong Wang
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China.
| |
Collapse
|
|
2
|
Motta-Romero HA, Perez-Donado CE, Auchtung JM, Rose DJ. Toxicity of cadmium on dynamic human gut microbiome cultures and the protective effect of cadmium-tolerant bacteria autochthonous to the gut. CHEMOSPHERE 2023; 338:139581. [PMID: 37474038 DOI: 10.1016/j.chemosphere.2023.139581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/22/2023]
Abstract
Cadmium (Cd) is a heavy metal toxic to the gut microbiome. In this study, we cultivated two human gut microbiomes (A and B) in bioreactors with Cd at 0 and 20 ppm for 7 days to investigate effects of Cd on the gut microbiome and to isolate Cd-tolerant bacteria autochthonous to the gut. Cd showed profound toxicity, abolishing butyrate production, depleting microbes in microbiome B, and simplifying microbiome A to a small Cd-tolerant community after 2 d of incubation. When spiked into the Cd-sensitive microbiome B, the Cd-tolerant community from microbiome A and isolates from that community worked synergistically with microbiome B to enhance butyrate production and maintained this synergism at Cd concentrations up to 5 ppm. Bacteria isolated from this Cd-tolerant community included Enterococcus faecium, Enterobacter cloacae, Lactococcus lactis, and Lactobacillus taiwanensis species. This work demonstrates a straightforward method for identifying Cd-tolerant bacteria autochthonous to the human gut that synergize with the microbiome to protect against Cd-related loss of butyrate production.
Collapse
Affiliation(s)
- Hollman A Motta-Romero
- Department of Food Science and Technology, University of Nebraska Lincoln, NE, USA; Nebraska Food for Health Center, University of Nebraska Lincoln, NE, USA
| | - Carmen E Perez-Donado
- Department of Food Science and Technology, University of Nebraska Lincoln, NE, USA; Nebraska Food for Health Center, University of Nebraska Lincoln, NE, USA
| | - Jennifer M Auchtung
- Department of Food Science and Technology, University of Nebraska Lincoln, NE, USA; Nebraska Food for Health Center, University of Nebraska Lincoln, NE, USA
| | - Devin J Rose
- Department of Food Science and Technology, University of Nebraska Lincoln, NE, USA; Nebraska Food for Health Center, University of Nebraska Lincoln, NE, USA; Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.
| |
Collapse
|