1
|
Etheridge T, Swiston C, Harrie RP, Bernstein PS. ACUTE POST-TRAUMATIC ENDOPHTHALMITIS SECONDARY TO BACILLUS PUMILUS / SAFENSIS. Retin Cases Brief Rep 2024; 18:305-307. [PMID: 36729827 DOI: 10.1097/icb.0000000000001391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 11/26/2022] [Indexed: 02/03/2023]
Abstract
PURPOSE To report a case of post-traumatic endophthalmitis secondary to Bacillus pumilus/safensis . METHODS Observational case report of a single patient. RESULTS A 62-year-old man presented with a traumatic corneal laceration because of baling wire while working on a sheep farm. Appropriate corneal laceration repair with injection of intravitreal antibiotics (ceftazidime, clindamycin, and vancomycin) was performed. A single organism, identified as B. pumilus or Bacillus safensis, was isolated from the vitreous aspirate. A subsequent pars plana vitrectomy, pars plana lensectomy, anterior capsulotomy, and fluid-air exchange was required because of severe inflammatory reaction from retained lens material, retinal edema, and vitreous opacities. Vision improved from hand motion to 20/60 at the three-month follow-up visit. CONCLUSION We describe a case of acute post-traumatic endophthalmitis secondary to B. pumilus/safensis.
Collapse
Affiliation(s)
- Tyler Etheridge
- John A. Moran Eye Center, University of Utah, Salt Lake City, Utah
| | | | | | | |
Collapse
|
2
|
Tirumalai MR. Education and public outreach: communicating science through storytelling. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2024; 25:e0020923. [PMID: 38661406 PMCID: PMC11044642 DOI: 10.1128/jmbe.00209-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/15/2024] [Indexed: 04/26/2024]
Abstract
Education and public outreach activities can be challenging for most active scientists, for very good reasons. Allotment of time to participate in outreach activities could be a major challenge. However, when such activities are incorporated into one's academic and research plan, they can be enriching. Here, the author describes his experience in what began as on one-off participation at an outreach event, leading to a series of speaking events addressing the public at the monthly meetings of several astronomy clubs/societies, observatories, etc. in the states of Texas, Louisiana, New Mexico, and Colorado. They have often involved the use of motifs and characters from popular science fiction, literature, and movies and when possible, getting the audience actively involved in the presentations. Furthermore, the discussions following each presentation have been enriching in terms of getting a broad perspective of the perceptions that people in general have, regarding the origins of life, microbiology, extremophiles, and astrobiology.
Collapse
Affiliation(s)
- Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| |
Collapse
|
3
|
Bin Hafeez A, Pełka K, Worobo R, Szweda P. In Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates. Int J Mol Sci 2024; 25:666. [PMID: 38203838 PMCID: PMC10780176 DOI: 10.3390/ijms25010666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Bacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence of virulence and antibiotic resistance properties, mobile genetic elements, and secondary metabolites. Functional annotation and Carbohydrate-Active enZYmes (CAZYme) profiling revealed the presence of genes and a repertoire of probiotics properties promoting enzymes. The isolates BB10.1, BP20.15 (isolated from bee bread), and PY2.3 (isolated from bee pollen) genome mining revealed the presence of several genes encoding acid, heat, cold, and other stress tolerance mechanisms, adhesion proteins required to survive and colonize harsh gastrointestinal environments, enzymes involved in the metabolism of dietary molecules, antioxidant activity, and genes associated with the synthesis of vitamins. In addition, genes responsible for the production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and other toxic compounds were also analyzed. Pan-genome analyses were performed with 180 Bacillus subtilis and 204 Bacillus velezensis genomes to mine for any novel genes present in the genomes of our isolates. Moreover, all three isolates also consisted of gene clusters encoding secondary metabolites.
Collapse
Affiliation(s)
- Ahmer Bin Hafeez
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| | - Karolina Pełka
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| | - Randy Worobo
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
| | - Piotr Szweda
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| |
Collapse
|
4
|
Tirumalai MR, Sivaraman RV, Kutty LA, Song EL, Fox GE. Ribosomal Protein Cluster Organization in Asgard Archaea. ARCHAEA (VANCOUVER, B.C.) 2023; 2023:5512414. [PMID: 38314098 PMCID: PMC10833476 DOI: 10.1155/2023/5512414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/31/2023] [Accepted: 09/08/2023] [Indexed: 02/06/2024]
Abstract
It has been proposed that the superphylum of Asgard Archaea may represent a historical link between the Archaea and Eukarya. Following the discovery of the Archaea, it was soon appreciated that archaeal ribosomes were more similar to those of Eukarya rather than Bacteria. Coupled with other eukaryotic-like features, it has been suggested that the Asgard Archaea may be directly linked to eukaryotes. However, the genomes of Bacteria and non-Asgard Archaea generally organize ribosome-related genes into clusters that likely function as operons. In contrast, eukaryotes typically do not employ an operon strategy. To gain further insight into conservation of the r-protein genes, the genome order of conserved ribosomal protein (r-protein) coding genes was identified in 17 Asgard genomes (thirteen complete genomes and four genomes with less than 20 contigs) and compared with those found previously in non-Asgard archaeal and bacterial genomes. A universal core of two clusters of 14 and 4 cooccurring r-proteins, respectively, was identified in both the Asgard and non-Asgard Archaea. The equivalent genes in the E. coli version of the cluster are found in the S10 and spc operons. The large cluster of 14 r-protein genes (uS19-uL22-uS3-uL29-uS17 from the S10 operon and uL14-uL24-uL5-uS14-uS8-uL6-uL18-uS5-uL30-uL15 from the spc operon) occurs as a complete set in the genomes of thirteen Asgard genomes (five Lokiarchaeotes, three Heimdallarchaeotes, one Odinarchaeote, and four Thorarchaeotes). Four less conserved clusters with partial bacterial equivalents were found in the Asgard. These were the L30e (str operon in Bacteria) cluster, the L18e (alpha operon in Bacteria) cluster, the S24e-S27ae-rpoE1 cluster, and the L31e, L12..L1 cluster. Finally, a new cluster referred to as L7ae was identified. In many cases, r-protein gene clusters/operons are less conserved in their organization in the Asgard group than in other Archaea. If this is generally true for nonribosomal gene clusters, the results may have implications for the history of genome organization. In particular, there may have been an early transition to or from the operon approach to genome organization. Other nonribosomal cellular features may support different relationships. For this reason, it may be important to consider ribosome features separately.
Collapse
Affiliation(s)
- Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
| | | | | | | | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
| |
Collapse
|
5
|
Laamarti M, Chemao-Elfihri MW, Essabbar A, Manni A, Kartti S, Alouane T, Temsamani L, Eljamali JE, Sbabou L, Ouadghiri M, Filali-Maltouf A, Belyamani L, Ibrahimi A. Genomic analysis of two Bacillus safensis isolated from Merzouga desert reveals desert adaptive and potential plant growth-promoting traits. Funct Integr Genomics 2022; 22:1173-1187. [PMID: 36175602 DOI: 10.1007/s10142-022-00905-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/04/2022]
Abstract
Deserts represent extreme environments for microorganisms, and conditions such as high soil salinity, nutrient deficiency, and increased levels of UV radiation make desert soil communities of high biotechnological potential. In this study, we isolated, sequenced, and assembled the genomes of Bacillus safensis strains BcP62 and Bcs93, to which we performed comparative genome analyses. Using the DDH and ANI of both strains with the available B. safensis genomes, we identified three potential subspecies within this group. Intra-species core genome phylogenetic analysis did not result in clustering genomes by niche type, with some exceptions. This study also revealed that the genomes of the analyzed strains possessed plant growth-promoting characteristics, most of which were conserved in all B. safensis strains. Furthermore, we highlight the genetic features of B. safensis BcP62 and Bcs93 related to survival in the Merzouga desert in Morocco. These strains could be potentially used in agriculture as PGPB in extreme environments, given their high tolerability to unfavorable conditions.
Collapse
Affiliation(s)
- Meriem Laamarti
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Mohammed Walid Chemao-Elfihri
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Abdelmounim Essabbar
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Amina Manni
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Souad Kartti
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Tarek Alouane
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Loubna Temsamani
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Jamal-Eddine Eljamali
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Laila Sbabou
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco.,Université Mohamned VI des Sciences de la Santé (UM6SS), Casablanca, Morocco
| | - Mouna Ouadghiri
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Abdelkarim Filali-Maltouf
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Lahcen Belyamani
- Université Mohamned VI des Sciences de la Santé (UM6SS), Casablanca, Morocco.,Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, Morocco. .,Université Mohamned VI des Sciences de la Santé (UM6SS), Casablanca, Morocco.
| |
Collapse
|
6
|
A Comparative Analysis of the Core Proteomes within and among the Bacillus subtilis and Bacillus cereus Evolutionary Groups Reveals the Patterns of Lineage- and Species-Specific Adaptations. Microorganisms 2022; 10:microorganisms10091720. [PMID: 36144322 PMCID: PMC9505155 DOI: 10.3390/microorganisms10091720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
By integrating phylogenomic and comparative analyses of 1104 high-quality genome sequences, we identify the core proteins and the lineage-specific fingerprint proteins of the various evolutionary clusters (clades/groups/species) of the Bacillus genus. As fingerprints, we denote those core proteins of a certain lineage that are present only in that particular lineage and absent in any other Bacillus lineage. Thus, these lineage-specific fingerprints are expected to be involved in particular adaptations of that lineage. Intriguingly, with a few notable exceptions, the majority of the Bacillus species demonstrate a rather low number of species-specific fingerprints, with the majority of them being of unknown function. Therefore, species-specific adaptations are mostly attributed to highly unstable (in evolutionary terms) accessory proteomes and possibly to changes at the gene regulation level. A series of comparative analyses consistently demonstrated that the progenitor of the Cereus Clade underwent an extensive genomic expansion of chromosomal protein-coding genes. In addition, the majority (76–82%) of the B. subtilis proteins that are essential or play a significant role in sporulation have close homologs in most species of both the Subtilis and the Cereus Clades. Finally, the identification of lineage-specific fingerprints by this study may allow for the future development of highly specific vaccines, therapeutic molecules, or rapid and low-cost molecular tests for species identification.
Collapse
|
7
|
Pangenome analyses of Bacillus pumilus, Bacillus safensis, and Priestia megaterium exploring the plant-associated features of bacilli strains isolated from canola. Mol Genet Genomics 2022; 297:1063-1079. [PMID: 35612623 DOI: 10.1007/s00438-022-01907-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/05/2022] [Indexed: 12/11/2022]
Abstract
Previous genome mining of the strains Bacillus pumilus 7PB, Bacillus safensis 1TAz, 8Taz, and 32PB, and Priestia megaterium 16PB isolated from canola revealed differences in the profile of antimicrobial biosynthetic genes when compared to the species type strains. To evaluate not only the similarities among B. pumilus, B. safensis, and P. megaterium genomes but also the specificities found in the canola bacilli, we performed comparative genomic analyses through the pangenome evaluation of each species. Besides that, other genome features were explored, especially focusing on plant-associated and biotechnological characteristics. The combination of the genome metrics Average Nucleotide Identity and digital DNA-DNA hybridization formulas 1 and 3 adopting the universal thresholds of 95 and 70%, respectively, was suitable to verify the identification of strains from these groups. On average, core genes corresponded to 45%, 52%, and 34% of B. pumilus, B. safensis, and P. megaterium open pangenomes, respectively. Many genes related to adaptations to plant-associated lifestyles were predicted, especially in the Bacillus genomes. These included genes for acetoin production, polyamines utilization, root exudate chemoreceptors, biofilm formation, and plant cell-wall degrading enzymes. Overall, we could observe that strains of these species exhibit many features in common, whereas most of their variable genome portions have features yet to be uncovered. The observed antifungal activity of canola bacilli might be a result of the synergistic action of secondary metabolites, siderophores, and chitinases. Genome analysis confirmed that these species and strains have biotechnological potential to be used both as agricultural inoculants or hydrolases producers. Up to our knowledge, this is the first work that evaluates the pangenome features of P. megaterium.
Collapse
|
8
|
Husni AAA, Ismail SI, Jaafar NM, Zulperi D. Current Classification of the Bacillus pumilus Group Species, the Rubber-Pathogenic Bacteria Causing Trunk Bulges Disease in Malaysia as Assessed by MLSA and Multi rep-PCR Approaches. THE PLANT PATHOLOGY JOURNAL 2021; 37:243-257. [PMID: 34111914 PMCID: PMC8200583 DOI: 10.5423/ppj.oa.02.2021.0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/22/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
Bacillus pumilus is the causal agent of trunk bulges disease affecting rubber and rubberwood quality and yield production. In this study, B. pumilus and other closely related species were included in B. pumilus group, as they shared over 99.5% similarity from 16S rRNA analysis. Multilocus sequence analysis (MLSA) of five housekeeping genes and repetitive elements-based polymerase chain reaction (rep-PCR) using REP, ERIC, and BOX primers conducted to analyze the diversity and systematic relationships of 20 isolates of B. pumilus group from four rubber tree plantations in Peninsular Malaysia (Serdang, Tanah Merah, Baling, and Rawang). Multi rep-PCR results revealed the genetic profiling among the B. pumilus group isolates, while MLSA results showed 98-100% similarity across the 20 isolates of B. pumilus group species. These 20 isolates, formerly established as B. pumilus, were found not to be grouped with B. pumilus. However, being distributed within distinctive groups of the B. pumilus group comprising of two clusters, A and B. Cluster A contained of 17 isolates close to B. altitudinis, whereas Cluster B consisted of three isolates attributed to B. safensis. This is the first MLSA and rep-PCR study on B. pumilus group, which provides an in-depth understanding of the diversity of these rubber-pathogenic isolates in Malaysia.
Collapse
Affiliation(s)
- Ainur Ainiah Azman Husni
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Siti Izera Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Noraini Md. Jaafar
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Dzarifah Zulperi
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
- Laboratory of Sustainable Resources Management, Institute of Tropical Forestry and Forest Products, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| |
Collapse
|
9
|
Fu X, Gong L, Liu Y, Lai Q, Li G, Shao Z. Bacillus pumilus Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation. Front Microbiol 2021; 12:571212. [PMID: 34025591 PMCID: PMC8139322 DOI: 10.3389/fmicb.2021.571212] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Background Members of the Bacillus pumilus group (abbreviated as the Bp group) are quite diverse and ubiquitous in marine environments, but little is known about correlation with their terrestrial counterparts. In this study, 16 marine strains that we had isolated before were sequenced and comparative genome analyses were performed with a total of 52 Bp group strains. The analyses included 20 marine isolates (which included the 16 new strains) and 32 terrestrial isolates, and their evolutionary relationships, differentiation, and environmental adaptation. Results Phylogenomic analysis revealed that the marine Bp group strains were grouped into three species: B. pumilus, B. altitudinis and B. safensis. All the three share a common ancestor. However, members of B. altitudinis were observed to cluster independently, separating from the other two, thus diverging from the others. Consistent with the universal nature of genes involved in the functioning of the translational machinery, the genes related to translation were enriched in the core genome. Functional genomic analyses revealed that the marine-derived and the terrestrial strains showed differences in certain hypothetical proteins, transcriptional regulators, K+ transporter (TrK) and ABC transporters. However, species differences showed the precedence of environmental adaptation discrepancies. In each species, land specific genes were found with possible functions that likely facilitate survival in diverse terrestrial niches, while marine bacteria were enriched with genes of unknown functions and those related to transcription, phage defense, DNA recombination and repair. Conclusion Our results indicated that the Bp isolates show distinct genomic features even as they share a common core. The marine and land isolates did not evolve independently; the transition between marine and non-marine habitats might have occurred multiple times. The lineage exhibited a priority effect over the niche in driving their dispersal. Certain intra-species niche specific genes could be related to a strains adaptation to its respective marine or terrestrial environment(s). In summary, this report describes the systematic evolution of 52 Bp group strains and will facilitate future studies toward understanding their ecological role and adaptation to marine and/or terrestrial environments.
Collapse
Affiliation(s)
- Xiaoteng Fu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Yang Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Guangyu Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| |
Collapse
|
10
|
Bryan NC, Lebreton F, Gilmore M, Ruvkun G, Zuber MT, Carr CE. Genomic and Functional Characterization of Enterococcus faecalis Isolates Recovered From the International Space Station and Their Potential for Pathogenicity. Front Microbiol 2021; 11:515319. [PMID: 33505359 PMCID: PMC7829349 DOI: 10.3389/fmicb.2020.515319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/09/2020] [Indexed: 01/07/2023] Open
Abstract
Enterococcus faecalis is a multidrug resistant, opportunistic human pathogen and a leading cause of hospital acquired infections. Recently, isolates have been recovered from the air and surfaces onboard the International Space Station (ISS). Pangenomic and functional analyses were carried out to assess their potential impact on astronaut health. Genomes of each ISS isolate, and both clinical and commensal reference strains, were evaluated for their core and unique gene content, acquired antibiotic resistance genes, phage, plasmid content, and virulence traits. In order to determine their potential survival when outside of the human host, isolates were also challenged with three weeks of desiccation at 30% relative humidity. Finally, pathogenicity of the ISS strains was evaluated in the model organism Caenorhabditis elegans. At the culmination of this study, there were no defining signatures that separated known pathogenic strains from the more commensal phenotypes using the currently available resources. As a result, the current reliance on database information alone must be shifted to experimentally evaluated genotypic and phenotypic characteristics of clinically relevant microorganisms.
Collapse
Affiliation(s)
- Noelle C. Bryan
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Francois Lebreton
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, MA, United States
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Michael Gilmore
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, MA, United States
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States
| | - Maria T. Zuber
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Christopher E. Carr
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States
- Georgia Institute of Technology, Atlanta, GA, United States
| |
Collapse
|
11
|
Nazli F, Jamil M, Hussain A, Hussain T. Exopolysaccharides and indole-3-acetic acid producing Bacillus safensis strain FN13 potential candidate for phytostabilization of heavy metals. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:738. [PMID: 33128189 DOI: 10.1007/s10661-020-08715-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 10/26/2020] [Indexed: 05/10/2023]
Abstract
Microbial population of soils irrigated with industrial wastewater may contain certain exopolysaccharides (EPS) and indole-3-acetic acid (IAA) producing bacterial strains having the ability to tolerate heavy metals along with plant growth-promoting (PGP) traits. As cadmium is one of the most toxic heavy metals for soils, plants, animals, and human beings, the present study was planned to isolate and characterize EPS- and IAA-producing, Cd-tolerant bacterial strains having tolerance against heavy metals along with plant growth-promoting traits. A total of 30 rhizobacterial strains (FN1-FN30) were isolated from rhizosphere soil collected from fields around industrial areas and roadsides irrigated with industrial wastewater. Out of these, eight isolates with the combined ability of IAA production and EPS production were characterized for PGP traits. On the basis of multifarious PGP traits and the results of root colonization assay, three most efficient EPS- and IAA-producing, Cd-tolerant plant growth-promoting strains, i.e., FN13, FN14, and FN16, were selected for multiple metal (Cd, Pb, Ni, and Cu) tolerance test along with quantification of growth, and IAA and EPS production abilities under Cd stress. Increasing levels of Cd stress negatively affected the tested characteristics of these strains, but FN13 showed more stability in growth, IAA production (18.24 μg mL-1), and EPS production (148.99 μg mL-1) compared to other strains under Cd stress. The morphological and biochemical analysis confirmed FN13 as Gram-positive, rod-shaped bacteria with smooth colonies of yellow appearance. The strain FN13 has strong root colonization (3.36 × 106 CFU g-1) ability for mustard seedlings and can solubilize Zn and phosphate along with the production of HCN, ammonia, and siderophores. The 16S rRNA sequencing confirmed it as the Bacillus safensis strain FN13. It can be explored as potential phytostabilizing biofertilizer for heavy metal-contaminated soils.
Collapse
Affiliation(s)
- Farheen Nazli
- Department of Soil Science, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan.
| | - Moazzam Jamil
- Department of Soil Science, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Azhar Hussain
- Department of Soil Science, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Tanveer Hussain
- Department of Forestry, Range and Wildlife Management, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| |
Collapse
|
12
|
Karpov DS, Osipova PG, Domashin AI, Polyakov NB, Solovyev AI, Zubasheva MV, Zhukhovitsky VG, Karpov VL, Poddubko SV, Novikova ND. Hyper-Resistance of the Bacillus licheniformis 24 Strain to Oxidative Stress Is Associated with Overexpression of Enzymatic Antioxidant System Genes. Mol Biol 2020. [DOI: 10.1134/s0026893320050040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
13
|
Seol D, Jhang SY, Kim H, Kim SY, Kwak HS, Kim SH, Lee W, Park S, Kim H, Cho S, Kwak W. Accurate and Strict Identification of Probiotic Species Based on Coverage of Whole-Metagenome Shotgun Sequencing Data. Front Microbiol 2019; 10:1683. [PMID: 31440213 PMCID: PMC6693478 DOI: 10.3389/fmicb.2019.01683] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 07/08/2019] [Indexed: 11/13/2022] Open
Abstract
Identifying the microbes present in probiotic products is an important issue in product quality control and public health. The most common methods used to identify genera containing species that produce lactic acid are matrix-assisted laser desorption/ionization–time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA sequence analysis. However, the high cost of operation, difficulty in distinguishing between similar species, and limitations of the current sequencing technologies have made it difficult to obtain accurate results using these tools. To overcome these problems, a whole-genome shotgun sequencing approach has been developed along with various metagenomic classification tools. Widely used tools include the marker gene and k-mer methods, but their inevitable false-positives (FPs) hampered an accurate analysis. We therefore, designed a coverage-based pipeline to reduce the FP problem and to achieve a more reliable identification of species. The coverage-based pipeline described here not only shows higher accuracy for the detection of species and proportion analysis, based on mapping depth, but can be applied regardless of the sequencing platform. We believe that the coverage-based pipeline described in this study can provide appropriate support for probiotic quality control, addressing current labeling issues.
Collapse
Affiliation(s)
- Donghyeok Seol
- C&K Genomics, Songpa-gu, South Korea.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - So Yun Jhang
- C&K Genomics, Songpa-gu, South Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Hyaekang Kim
- C&K Genomics, Songpa-gu, South Korea.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Se-Young Kim
- R&D Center, CTCBIO, Inc., Hwaseong-si, South Korea
| | - Hyo-Sun Kwak
- Division of Microbiology, Ministry of Food and Drug Safety, Cheongju-si, South Korea
| | - Soon Han Kim
- Division of Microbiology, Ministry of Food and Drug Safety, Cheongju-si, South Korea
| | - Woojung Lee
- Division of Microbiology, Ministry of Food and Drug Safety, Cheongju-si, South Korea
| | - Sewook Park
- Division of Microbiology, Ministry of Food and Drug Safety, Cheongju-si, South Korea
| | - Heebal Kim
- C&K Genomics, Songpa-gu, South Korea.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Seoae Cho
- C&K Genomics, Songpa-gu, South Korea
| | | |
Collapse
|
14
|
Reply to Mortazavi, “Acquired Antibiotic Resistance in
Escherichia coli
Exposed to Simulated Microgravity: Possible Role of Other Space Stressors and Adaptive Responses”. mBio 2019; 10:mBio.00391-19. [PMID: 30914512 PMCID: PMC6437056 DOI: 10.1128/mbio.00391-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|