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Miliotis G, Sengupta P, Hameed A, Chuvochina M, McDonagh F, Simpson AC, Parker CW, Singh NK, Rekha PD, Morris D, Raman K, Kyrpides NC, Hugenholtz P, Venkateswaran K. Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov. mBio 2024; 15:e0018124. [PMID: 38477597 PMCID: PMC11005411 DOI: 10.1128/mbio.00181-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 03/14/2024] Open
Abstract
A comprehensive microbial surveillance was conducted at NASA's Mars 2020 spacecraft assembly facility (SAF), where whole-genome sequencing (WGS) of 110 bacterial strains was performed. One isolate, designated 179-BFC-A-HST, exhibited less than 80% average nucleotide identity (ANI) to known species, suggesting a novel organism. This strain demonstrated high-level resistance [minimum inhibitory concentration (MIC) >256 mg/L] to third-generation cephalosporins, including ceftazidime, cefpodoxime, combination ceftazidime/avibactam, and the fourth-generation cephalosporin cefepime. The results of a comparative genomic analysis revealed that 179-BFC-A-HST is most closely related to Virgibacillus halophilus 5B73CT, sharing an ANI of 78.7% and a digital DNA-DNA hybridization (dDDH) value of 23.5%, while their 16S rRNA gene sequences shared 97.7% nucleotide identity. Based on these results and the recent recognition that the genus Virgibacillus is polyphyletic, strain 179-BFC-A-HST is proposed as a novel species of a novel genus, Tigheibacillus jepli gen. nov., sp. nov (type strain 179-BFC-A-HST = DSM 115946T = NRRL B-65666T), and its closest neighbor, V. halophilus, is proposed to be reassigned to this genus as Tigheibacillus halophilus comb. nov. (type strain 5B73CT = DSM 21623T = JCM 21758T = KCTC 13935T). It was also necessary to reclassify its second closest neighbor Virgibacillus soli, as a member of a novel genus Paracerasibacillus, reflecting its phylogenetic position relative to the genus Cerasibacillus, for which we propose Paracerasibacillus soli comb. nov. (type strain CC-YMP-6T = DSM 22952T = CCM 7714T). Within Amphibacillaceae (n = 64), P. soli exhibited 11 antibiotic resistance genes (ARG), while T. jepli encoded for 3, lacking any known β-lactamases, suggesting resistance from variant penicillin-binding proteins, disrupting cephalosporin efficacy. P. soli was highly resistant to azithromycin (MIC >64 mg/L) yet susceptible to cephalosporins and penicillins. IMPORTANCE The significance of this research extends to understanding microbial survival and adaptation in oligotrophic environments, such as those found in SAF. Whole-genome sequencing of several strains isolated from Mars 2020 mission assembly cleanroom facilities, including the discovery of the novel species Tigheibacillus jepli, highlights the resilience and antimicrobial resistance (AMR) in clinically relevant antibiotic classes of microbes in nutrient-scarce settings. The study also redefines the taxonomic classifications within the Amphibacillaceae family, aligning genetic identities with phylogenetic data. Investigating ARG and virulence factors (VF) across these strains illuminates the microbial capability for resistance under resource-limited conditions while emphasizing the role of human-associated VF in microbial survival, informing sterilization practices and microbial management in similar oligotrophic settings beyond spacecraft assembly cleanrooms such as pharmaceutical and medical industry cleanrooms.
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Affiliation(s)
- Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Asif Hameed
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Australia
| | - Francesca McDonagh
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Anna C. Simpson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Ceth W. Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Punchappady D. Rekha
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Nikos C. Kyrpides
- US Department of Energy Joint Genome Institute, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Australia
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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Marimuthu S, Puvaneswari S, Lakshmanan R. Effect of Biofloc Technology Enriches the Growth of Litopenaeus vannamei (Boone, 1931). Appl Biochem Biotechnol 2023:10.1007/s12010-023-04729-x. [PMID: 37792176 DOI: 10.1007/s12010-023-04729-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2023] [Indexed: 10/05/2023]
Abstract
The use of probiotics in shrimp farms has expanded as an alternative to antibiotics, improving shrimp health, growth, disease control and water quality. However, the efficacy of probiotics in intensive systems using biofloc remains uncertain. This study investigated bioremediation and biocontrol of commercial probiotics using biofloc, analysing water quality and bacterial groups influencing shrimp performance. Thirteen microbial colonies were observed in the biofloc samples, and their evolutionary history was inferred using the neighbour-joining method. Analysis using MEGA6 software revealed 99.6% similarity between colony 1P1 and Virgibacillus sp. and 99.8% similarity between colony 2P2 and Bacillus kochii. The study analysed the biochemical and amino acid content of shrimp cultured using biofloc technology for 85 days. The study found that biofloc-cultured L. Vannamei flesh had higher levels of moisture (31%), ash (15.2%), protein (34%) and lipid (12.6%). No seasonal variations were observed between biofloc samples in winter and summer seasons. Protein levels were found to be appropriate for shrimp growth in both ex situ and in situ biofloc systems. The average growth rate (kg/m2) of biofloc-cultured shrimp was significantly greater than in normal pond shrimp in both samples. The feed conversion ratio in the biofloc tank was lower than in the usual pond-cultured shrimp, possibly due to lower growth rate, lower feeding frequency (2 times per day) and higher density. The growth of L. vannamei shrimp is influenced by stocking density, with higher stocking density affecting the average weight. The study also examined the growth biochemical and amino acid content of shrimp cultured using biofloc technology.
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Affiliation(s)
| | - Subramanian Puvaneswari
- Department of Zoology, Annamalai University, Chidambaram, 608002, Tamil Nadu, India.
- Department of Zoology, Dharmapuram Gnanambigai Govt. Arts College for Women, Mayiladuthurai, 609001, Tamil Nadu, India.
| | - Ramamoorthy Lakshmanan
- Department of Zoology, Dharmapuram Gnanambigai Govt. Arts College for Women, Mayiladuthurai, 609001, Tamil Nadu, India
- CAS in Marine Biology, Annamalai University, Parangipettai, 608502, Tamil Nadu, India
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Ashfaq MY, Da'na DA, Al-Ghouti MA. Application of MALDI-TOF MS for identification of environmental bacteria: A review. J Environ Manage 2022; 305:114359. [PMID: 34959061 DOI: 10.1016/j.jenvman.2021.114359] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/07/2021] [Accepted: 12/18/2021] [Indexed: 05/22/2023]
Abstract
Bacteria play a variety of roles in the environment. They maintain the balance in the ecosystem and provide different ecosystem services such as in biogeochemical cycling of nutrients, biodegradation of toxic pollutants, and others. Therefore, isolation and identification of different environmental bacteria are important to most environmental research. Due to the high cost and time associated with the conventional molecular techniques, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has gained considerable attention for routine identification of bacteria. This review aims to provide an overview of the application of MALDI-TOF MS in various environmental studies through bibliometric analysis and literature review. The bibliometric analysis helped to understand the time-variable application of MALDI-TOF MS in various environmental studies. The categorical literature review covers various environmental studies comprising areas like ecology, food microbiology, environmental biotechnology, agriculture, and plant sciences, which show the application of the technique for identification and characterization of pollutant-degrading, plant-associated, disease-causing, soil-beneficial, and other environmental bacteria. Further research should focus on bridging the gap between the phylogenetic identity of bacteria and their specific environmental functions or metabolic traits that can help in rapid advancements in environmental research, thereby, improving time and cost savings.
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Affiliation(s)
- Mohammad Y Ashfaq
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Dana A Da'na
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Mohammad A Al-Ghouti
- Environmental Science program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar.
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