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Kwon KM, Kim EH, Sim KH, Lee YJ, Kang EJ, Han KH, Jin JS, Kim DK, Ahn JH, Hwang IH. Phenylacetic acid, an anti-vaginitis metabolite produced by the vaginal symbiotic bacterium Chryseobacterium gleum. Sci Rep 2024; 14:12226. [PMID: 38806600 PMCID: PMC11133378 DOI: 10.1038/s41598-024-62947-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 05/22/2024] [Indexed: 05/30/2024] Open
Abstract
The human microbiome contains genetic information that regulates metabolic processes in response to host health and disease. While acidic vaginal pH is maintained in normal conditions, the pH level increases in infectious vaginitis. We propose that this change in the vaginal environment triggers the biosynthesis of anti-vaginitis metabolites. Gene expression levels of Chryseobacterium gleum, a vaginal symbiotic bacterium, were found to be affected by pH changes. The distinctive difference in the metabolic profiles between two C. gleum cultures incubated under acidic and neutral pH conditions was suggested to be an anti-vaginitis molecule, which was identified as phenylacetic acid (PAA) by spectroscopic data analysis. The antimicrobial activity of PAA was evaluated in vitro, showing greater toxicity toward Gardnerella vaginalis and Candida albicans, two major vaginal pathogens, relative to commensal Lactobacillus spp. The activation of myeloperoxidase, prostaglandin E2, and nuclear factor-κB, and the expression of cyclooxygenase-2 were reduced by an intravaginal administration of PAA in the vaginitis mouse model. In addition, PAA displayed the downregulation of mast cell activation. Therefore, PAA was suggested to be a messenger molecule that mediates interactions between the human microbiome and vaginal health.
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Affiliation(s)
- Kang Mu Kwon
- Department of Pharmacy, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea
| | - Eun-Hye Kim
- Department of Korean Pharmacy, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea
| | - Kyeong Hwa Sim
- Department of Pharmacology, School of Medicine, Daegu Catholic University, 33 Duryugongwon-ro 17-gil, Nam-gu, Daegu, 42472, Republic of Korea
| | - Youn Ju Lee
- Department of Pharmacology, School of Medicine, Daegu Catholic University, 33 Duryugongwon-ro 17-gil, Nam-gu, Daegu, 42472, Republic of Korea
| | - Eun-Ji Kang
- Department of Food and Biotechnology, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea
| | - Kap-Hoon Han
- Department of Pharmaceutical Engineering, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea
| | - Jong-Sik Jin
- Department of Oriental Medicine Resources, Jeonbuk National University, Iksan, Jeonbuk, 54596, Republic of Korea
| | - Dae Keun Kim
- Department of Pharmacy, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea
- Research Institute of Pharmaceutical Sciences, Woosuk University, Wanju, 55338, Republic of Korea
| | - Ji-Hye Ahn
- Department of Korean Pharmacy, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea.
| | - In Hyun Hwang
- Department of Pharmacy, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea.
- Research Institute of Pharmaceutical Sciences, Woosuk University, Wanju, 55338, Republic of Korea.
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Kong T, Fan X, Tran NT. Changes in Hemolymph Microbiota of Chinese Mitten Crab ( Eriocheir sinensis) in Response to Aeromonas hydrophila or Staphylococcus aureus Infection. Animals (Basel) 2023; 13:3058. [PMID: 37835665 PMCID: PMC10571569 DOI: 10.3390/ani13193058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
The Chinese mitten crab (Eriocheir sinensis) has significant economic potential in both the Chinese domestic and global markets. The hemolymph microbiota is known to play a critical role in regulating physiological and biochemical functions in crustaceans. However, the study of the hemolymph microbiota of E. sinensis in response to infections has not been undertaken. In this study, changes in the composition and function of the hemolymph microbiota in E. sinensis infected with either Staphylococcus aureus (Sa) or Aeromonas hydrophila (Ah) were investigated using 16S rRNA sequencing, with a phosphate buffer saline (PBS) injection serving as the control. Results showed that the dominant hemolymph microbiota of E. sinensis were Proteobacteria, Bacteroidota, and Firmicutes. The relative abundance of the phyla Firmicutes, Bdellovibrionota, and Myxococcota was significantly reduced in both Sa and Ah groups compared to the PBS group. At the genus level, compared to the PBS group, a significant increase in the abundance of Flavobacterium and Aeromonas was found in both Ah and Sa groups. The analysis of the functional profile showed that pathways related to 'cell growth and death', 'metabolism of terpenoids and polyketides', 'cancers', 'lipid metabolism', 'neurodegenerative diseases', 'metabolism of other amino acids', 'xenobiotics biodegradation and metabolism', and 'circulatory system and endocrine system' were predominant in the Ah group. Meanwhile, pathways related to 'metabolism or genetic information progressing', such as 'translation', 'metabolic diseases', and 'cellular processes and signaling', were enriched in the Sa group. This study revealed the effects of pathogens (S. aureus or A. hydrophila) on the maintenance of the hemolymph microbiota in E. sinensis. It shed light on the mechanisms employed by the hemolymph microbiota of E. sinensis under pathogen stimulation.
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Affiliation(s)
- Tongtong Kong
- School of Life Sciences, Qufu Normal University, Qufu 273165, China; (T.K.)
| | - Xinyue Fan
- School of Life Sciences, Qufu Normal University, Qufu 273165, China; (T.K.)
| | - Ngoc Tuan Tran
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou 515063, China
- Institute of Marine Sciences, Shantou University, Shantou 515063, China
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Irfan M, Tariq M, Basharat Z, Abid Khan RM, Jahanzaeb M, Shakeel M, Nisa ZU, Shahzad M, Jahanzaib M, Moin ST, Hassan SS, Khan IA. Genomic analysis of Chryseobacterium indologenes and conformational dynamics of the selected DD-peptidase. Res Microbiol 2023; 174:103990. [PMID: 36087828 DOI: 10.1016/j.resmic.2022.103990] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/27/2022] [Accepted: 08/30/2022] [Indexed: 01/11/2023]
Abstract
Chrysobacterium indologenes is an emerging MDR pathogen that belongs to the family Flavobacteriaceae. The genome of the C. indologenes, isolated from the nephrotic patient, was sequenced through Illumina MiSeq. The pangenomics of available 56 C. indologenes strains using BPGA revealed an open pangenome (n=5553 CDS), core genome (2141), and accessory genome (2013). The CEG/DEG database identified 662 essential genes that drastically reduced to 68 genes after non-homology analyses towards human and gut microbiome. Further filtering the data for other drug target prioritizing parameters resulted in 32 putative targets. Keeping in view the crucial role played in cell wall biosynthesis, dacB was selected as the final target that encodes D-alanyl-d-alanine carboxypeptidase/endopeptidase (DD-peptidase). The 3D structure of dacB was modelled and rendered to docking analyses against two compound libraries of African plants (n=6842) and Tibetan medicines (n=52). The ADMET profiling exhibited the physicochemical properties of final compounds. The MD simulations showed the stability of inhibitor-DD-peptidase complex and interactions in terms of RMSD, RMSF, binding free energy calculation and H-bonding. We propose that the novel compounds Leptopene and ZINC95486338 from our findings might be potent DD-peptidase inhibitors that could aid in the development of new antibiotic-resistant therapy for the emerging MDR C. indologenes.
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Affiliation(s)
- Muhammad Irfan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Muhammad Tariq
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Zarrin Basharat
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan.
| | - Rao Muhammad Abid Khan
- Department of Clinical Microbiology, Sindh Institute of Urology & Transplantation (SIUT), Karachi, Pakistan
| | - Muhammad Jahanzaeb
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Muhammad Shakeel
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Zaib Un Nisa
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Mohsin Shahzad
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Muhammad Jahanzaib
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Syed Tarique Moin
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Syed Shah Hassan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Ishtiaq Ahmad Khan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan.
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Sylvain FÉ, Leroux N, Normandeau É, Holland A, Bouslama S, Mercier PL, Luis Val A, Derome N. Genomic and Environmental Factors Shape the Active Gill Bacterial Community of an Amazonian Teleost Holobiont. Microbiol Spectr 2022; 10:e0206422. [PMID: 36445161 PMCID: PMC9769777 DOI: 10.1128/spectrum.02064-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
Fish bacterial communities provide functions critical for their host's survival in contrasting environments. These communities are sensitive to environmental-specific factors (i.e., physicochemical parameters, bacterioplankton), and host-specific factors (i.e., host genetic background). The relative contribution of these factors shaping Amazonian fish bacterial communities is largely unknown. Here, we investigated this topic by analyzing the gill bacterial communities of 240 wild flag cichlids (Mesonauta festivus) from 4 different populations (genetic clusters) distributed across 12 sites in 2 contrasting water types (ion-poor/acidic black water and ion-rich/circumneutral white water). Transcriptionally active gill bacterial communities were characterized by a 16S rRNA metabarcoding approach carried on RNA extractions. They were analyzed using comprehensive data sets from the hosts genetic background (Genotyping-By-Sequencing), the bacterioplankton (16S rRNA) and a set of 34 environmental parameters. Results show that the taxonomic structure of 16S rRNA gene transcripts libraries were significantly different between the 4 genetic clusters and also between the 2 water types. However, results suggest that the contribution of the host's genetic background was relatively weak in comparison to the environment-related factors in structuring the relative abundance of different active gill bacteria species. This finding was also confirmed by a mixed-effects modeling analysis, which indicated that the dissimilarity between the taxonomic structure of bacterioplanktonic communities possessed the best explicative power regarding the dissimilarity between gill bacterial communities' structure, while pairwise fixation indexes (FST) from the hosts' genetic data only had a weak explicative power. We discuss these results in terms of bacterial community assembly processes and flag cichlid fish ecology. IMPORTANCE Host-associated microbial communities respond to factors specific to the host physiology, genetic backgrounds, and life history. However, these communities also show different degrees of sensitivity to environment-dependent factors, such as abiotic physico-chemical parameters and ecological interactions. The relative importance of host- versus environment-associated factors in shaping teleost bacterial communities is still understudied and is paramount for their conservation and aquaculture. Here, we studied the relative importance of host- and environment-associated factors structuring teleost bacterial communities using gill samples from a wild Amazonian teleost model (Mesonauta festivus) sampled in contrasting habitats along a 1500 km section of the Amazonian basin, thus ensuring high genetic diversity. Results showed that the contribution of the host's genetic background was weak compared to environment-related bacterioplanktonic communities in shaping gill bacterial assemblages, thereby suggesting that our understanding of teleost microbiome assembly could benefit from further studies focused on the ecological interplay between host-associated and free-living communities.
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Affiliation(s)
| | - Nicolas Leroux
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Éric Normandeau
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Aleicia Holland
- La Trobe University, School of Life Science, Department of Ecology, Environment and Evolution, Centre for Freshwater Ecosystems, Wodonga, Victoria, Australia
| | - Sidki Bouslama
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Pierre-Luc Mercier
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Adalberto Luis Val
- Instituto Nacional de Pesquisas da Amazônia (INPA), Laboratório de Ecofisiologia e Evolução Molecular, Manaus, Amazonas, Brazil
| | - Nicolas Derome
- Instituto Nacional de Pesquisas da Amazônia (INPA), Laboratório de Ecofisiologia e Evolução Molecular, Manaus, Amazonas, Brazil
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Andreeva SV, Filippova YY, Devyatova EV, Nokhrin DY. Variability of the structure of winter microbial communities in Chelyabinsk lakes. BIOSYSTEMS DIVERSITY 2021. [DOI: 10.15421/10.15421/012139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Microorganisms form complex and dynamic communities that play a key role in the biogeochemical cycles of lakes. A high level of urbanization is currently a serious threat to bacterial communities and the ecosystem of freshwater bodies. To assess the contribution of anthropogenic load to variations in the structure of winter microbial communities in lakes, microorganisms of four water bodies of Chelyabinsk region were studied for the first time. We used cultural, chromatography-mass spectrometric, and modern methods of statistical data processing (particularly, multivariate exploratory analysis and canonical analysis of correspondences). The research showed that the composition of winter microbial communities in lakes Chebarkul’, Smolino, Pervoye, and Shershenevskoye Reservoir did not differ significantly between the main phyla of microorganisms. The dominant microorganisms were found to be of the Firmicutes phylum and Actinobacteria phylum. The structure of bacterial communities had special features depending on the characteristics of the water body and the sampling depths. Thus, in the lakes Smolino, Pervoye, and Shershenevskoye Reservoir, an important role was played by associations between microorganisms – indicators of fecal contamination: coliform bacteria and Enterococcus. On the contrary, in Chebarkul’ Lake, members of the genus Bacillus, which are natural bioremediators, formed stable winter associations. However, the differences between water bodies and sampling depths reflected 28.1% and 9.8% of the variability of the winter microbial communities, respectively. The largest contribution (about 60%) to the variability of the structure was made by intra-water processes, which determined the high heterogeneity of samples from different water areas. We assume that an important role in this variability was played by the high anthropogenic impact in a large industrial metropolis. In our opinion, this line of research is very promising for addressing key environmental issues.
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Andreeva SV, Filippova YY, Devyatova EV, Nokhrin DY. Variability of the structure of winter microbial communities in Chelyabinsk lakes. BIOSYSTEMS DIVERSITY 2021. [DOI: 10.15421/012139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Microorganisms form complex and dynamic communities that play a key role in the biogeochemical cycles of lakes. A high level of urbanization is currently a serious threat to bacterial communities and the ecosystem of freshwater bodies. To assess the contribution of anthropogenic load to variations in the structure of winter microbial communities in lakes, microorganisms of four water bodies of Chelyabinsk region were studied for the first time. We used cultural, chromatography-mass spectrometric, and modern methods of statistical data processing (particularly, multivariate exploratory analysis and canonical analysis of correspondences). The research showed that the composition of winter microbial communities in lakes Chebarkul’, Smolino, Pervoye, and Shershenevskoye Reservoir did not differ significantly between the main phyla of microorganisms. The dominant microorganisms were found to be of the Firmicutes phylum and Actinobacteria phylum. The structure of bacterial communities had special features depending on the characteristics of the water body and the sampling depths. Thus, in the lakes Smolino, Pervoye, and Shershenevskoye Reservoir, an important role was played by associations between microorganisms – indicators of fecal contamination: coliform bacteria and Enterococcus. On the contrary, in Chebarkul’ Lake, members of the genus Bacillus, which are natural bioremediators, formed stable winter associations. However, the differences between water bodies and sampling depths reflected 28.1% and 9.8% of the variability of the winter microbial communities, respectively. The largest contribution (about 60%) to the variability of the structure was made by intra-water processes, which determined the high heterogeneity of samples from different water areas. We assume that an important role in this variability was played by the high anthropogenic impact in a large industrial metropolis. In our opinion, this line of research is very promising for addressing key environmental issues.
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Clinton M, Wyness AJ, Martin SAM, Brierley AS, Ferrier DEK. Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs. BMC Microbiol 2021; 21:313. [PMID: 34758745 PMCID: PMC8579561 DOI: 10.1186/s12866-021-02374-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022] Open
Abstract
Background Understanding the influence of methodology on results is an essential consideration in experimental design. In the expanding field of fish microbiology, many best practices and targeted techniques remain to be refined. This study aimed to compare microbial assemblages obtained from Atlantic salmon (Salmo salar) gills by swabbing versus biopsy excision. Results demonstrate the variation introduced by altered sampling strategies and enhance the available knowledge of the fish gill microbiome. Results The microbiome was sampled using swabs and biopsies from fish gills, with identical treatment of samples for 16S next generation Illumina sequencing. Results show a clear divergence in microbial communities obtained through the different sampling strategies, with swabbing consistently isolating a more diverse microbial consortia, and suffering less from the technical issue of host DNA contamination associated with biopsy use. Sequencing results from biopsy-derived extractions, however, hint at the potential for more cryptic localisation of some community members. Conclusions Overall, results demonstrate a divergence in the obtained microbial community when different sampling methodology is used. Swabbing appears a superior method for sampling the microbiota of mucosal surfaces for broad ecological research in fish, whilst biopsies might be best applied in exploration of communities beyond the reach of swabs, such as sub-surface and intracellular microbes, as well as in pathogen diagnosis. Most studies on the external microbial communities of aquatic organisms utilise swabbing for sample collection, likely due to convenience. Much of the ultrastructure of gill tissue in live fish is, however, potentially inaccessible to swabbing, meaning swabbing might fail to capture the full diversity of gill microbiota. This work therefore also provides valuable insight into partitioning of the gill microbiota, informing varied applications of different sampling methods in experimental design for future research. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02374-0.
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Affiliation(s)
- Morag Clinton
- Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK. .,Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA.
| | - Adam J Wyness
- Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK.,Coastal Research Group, Department of Zoology and Entomology, Rhodes University, Makhanda (Grahamstown), 6139, South Africa
| | - Samuel A M Martin
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Andrew S Brierley
- Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK
| | - David E K Ferrier
- Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK.
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War of the microbial world: Acanthamoeba spp. interactions with microorganisms. Folia Microbiol (Praha) 2021; 66:689-699. [PMID: 34145552 PMCID: PMC8212903 DOI: 10.1007/s12223-021-00889-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 06/09/2021] [Indexed: 12/15/2022]
Abstract
Acanthamoeba is known to interact with a plethora of microorganisms such as bacteria, fungi and viruses. In these interactions, the amoebae can be predatory in nature, transmission vehicle or an incubator. Amoebae consume microorganisms, especially bacteria, as food source to fulfil their nutritional needs by taking up bacteria through phagocytosis and lysing them in phagolysosomes and hence play an eminent role in the regulation of bacterial density in the nature and accountable for eradication of around 60% of the bacterial population in the environment. Acanthamoeba can also act as a “Trojan horse” for microbial transmission in the environment. Additionally, Acanthamoeba may serve as an incubator-like reservoir for microorganisms, including those that are pathogenic to humans, where the microorganisms use amoebae’s defences to resist harsh environment and evade host defences and drugs, whilst growing in numbers inside the amoebae. Furthermore, amoebae can also be used as a “genetic melting pot” where exchange of genes as well as adaptation of microorganisms, leading to higher pathogenicity, may arise. Here, we describe bacteria, fungi and viruses that are known to interact with Acanthamoeba spp.
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