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Tariq M, Jameel F, Ijaz U, Abdullah M, Rashid K. Biofertilizer microorganisms accompanying pathogenic attributes: a potential threat. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:77-90. [PMID: 35221573 PMCID: PMC8847475 DOI: 10.1007/s12298-022-01138-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 11/30/2021] [Accepted: 01/14/2022] [Indexed: 05/04/2023]
Abstract
Application of biofertilizers containing living or dormant plant growth promoting bacterial cells is considered to be an ecofriendly alternative of chemical fertilizers for improved crop production. Biofertilizers opened myriad doors towards sustainable agriculture as they effectively reduce heavy use of chemical fertilizers and pesticides by keeping soils profuse in micro and macronutrients, regulating plant hormones and restraining infections caused by the pests present in soil without inflicting environmental damage. Generally, pathogenicity and biosafety testing of potential plant growth promoting bacteria (PGPB) are not performed, and the bacteria are reported to be beneficial solely on testing plant growth promoting characteristics. Unfortunately, some rhizosphere and endophytic PGPB are reported to be involved in various diseases. Such PGPB can also spread virulence and multidrug resistance genes carried by them through horizontal gene transfer to other bacteria in the environment. Therefore, deployment of such microbial populations in open fields could lead to disastrous side effects on human health and environment. Careless declaration of bacteria as PGPB is more pronounced in research publications. Here, we present a comprehensive report of declared PGPB which are reported to be pathogenic in other studies. This review also suggests the employment of some additional safety assessment protocols before reporting a bacteria as beneficial and product development.
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Affiliation(s)
- Mohsin Tariq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Farwah Jameel
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Usman Ijaz
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Muhammad Abdullah
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Kamran Rashid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
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Kaitala V, Koivu-Jolma M, Laakso J. Infective prey leads to a partial role reversal in a predator-prey interaction. PLoS One 2021; 16:e0249156. [PMID: 34534219 PMCID: PMC8448379 DOI: 10.1371/journal.pone.0249156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/02/2021] [Indexed: 11/18/2022] Open
Abstract
An infective prey has the potential to infect, kill and consume its predator. Such a prey-predator relationship fundamentally differs from the predator-prey interaction because the prey can directly profit from the predator as a growth resource. Here we present a population dynamics model of partial role reversal in the predator-prey interaction of two species, the bottom dwelling marine deposit feeder sea cucumber Apostichopus japonicus and an important food source for the sea cucumber but potentially infective bacterium Vibrio splendidus. We analyse the effects of different parameters, e.g. infectivity and grazing rate, on the population sizes. We show that relative population sizes of the sea cucumber and V. Splendidus may switch with increasing infectivity. We also show that in the partial role reversal interaction the infective prey may benefit from the presence of the predator such that the population size may exceed the value of the carrying capacity of the prey in the absence of the predator. We also analysed the conditions for species extinction. The extinction of the prey, V. splendidus, may occur when its growth rate is low, or in the absence of infectivity. The extinction of the predator, A. japonicus, may follow if either the infectivity of the prey is high or a moderately infective prey is abundant. We conclude that partial role reversal is an undervalued subject in predator-prey studies.
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Affiliation(s)
- Veijo Kaitala
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Helsinki University, Helsinki, Finland
- * E-mail:
| | - Mikko Koivu-Jolma
- Department of Physics, Faculty of Science, Helsinki University, Helsinki, Finland
| | - Jouni Laakso
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Helsinki University, Helsinki, Finland
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Shobo CO, Alisoltani A, Abia ALK, Mtshali PS, Ismail A, Zishiri O, Horn JD, Brysiewicz P, Essack SY, Bester LA. Bacterial diversity and functional profile of microbial populations on surfaces in public hospital environments in South Africa: A high throughput metagenomic analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 719:137360. [PMID: 32114226 DOI: 10.1016/j.scitotenv.2020.137360] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
With the introduction of the One Health approach to global health advocated by the World Health Organization, the role of the environment as a reservoir and transmission route for diverse microorganisms is increasingly being recognised globally. This study investigated the diversity and functional profiles of bacterial communities using high-throughput metagenomics of the 16S rRNA gene in samples collected from environmental surfaces in different levels of healthcare in South Africa. A total of 150 samples were collected in three public hospitals [District (A), Regional (C) and Central (B)] from intensive care and paediatric wards. Military hospitals were excluded. Swabs were taken from mattresses, drip stands, ward telephones, patient files and sinks. A total of 7,996,346 reads were found, of which 7,319,569 were quality-filtered reads. Unique (and shared) microbial community structures were identified within the different hospital levels, locations and sample source. A total of 11 phyla, 29 classes, 50 orders, 105 families, 190 genera and 288 known species were identified. The primary phyla identified were Proteobacteria, Firmicutes and Actinobacteria. The dominant class identified was Gamma-proteobacteria, followed by Bacilli and Actinobacteria. Acinetobacter (16.08%), Citrobacter (13.64%), Staphylococcus (9.65%) and Corynebacterium (6.15%) were predominant genera. Although the functional profile analysis identified citrate cycle (TCA), signal transduction mechanisms, bisphenol degradation, tyrosine metabolism and transcription-factors as the dominant pathways, human disease functional classes, including involvement in antibiotic resistance, were significantly identified. The drip stands, patient files and ward telephones in all the wards of Hospitals A and C contained a higher number of human diseases functional classes. These findings highlight the potential of different hospital environments to serve as reservoirs and possible sources of bacterial pathogens; thus, the need for better monitoring and hygienic practices within the hospital environment.
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Affiliation(s)
- Christiana Omowunmi Shobo
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Medical Microbiology, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Arghavan Alisoltani
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Philip Senzo Mtshali
- Sequencing Core Facility, National Institute for Communicable Diseases, Division of National Health Laboratory Service, Sandringham, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, Division of National Health Laboratory Service, Sandringham, Johannesburg, South Africa
| | - Oliver Zishiri
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
| | - Juliana Deidre Horn
- South Africa Military Health Service, Area Military Health Care, KwaZulu-Natal, Durban, South Africa
| | - Petra Brysiewicz
- Discipline of Nursing, School of Nursing & Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Sabiha Yusuf Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Linda Antoinette Bester
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
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Adewumi AT, Ramharack P, Soremekun OS, Soliman MES. Delving into the Characteristic Features of "Menace" Mycobacterium tuberculosis Homologs: A Structural Dynamics and Proteomics Perspectives. Protein J 2020; 39:118-132. [PMID: 32162114 DOI: 10.1007/s10930-020-09890-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The global increase in the morbidity/mortality rate of Mycobacterial infections, predominantly renascent tuberculosis, leprosy, and Buruli ulcers have become worrisome over the years. More challenging is the incidence of resistance mediated by mutant Mycobacterium strains against front-line antitubercular drugs. Homologous to all Mycobacteria species is the GlcNAc-6-phosphate deacetylase (NagA) which catalyzes essential amino sugars synthesis required for cell wall architecture, hence, metamorphosing into an important pharmacological target for curtailing virulence and drug-resistance. This study used integrated bioinformatics methods, MD simulations, and DynaMut and PolyPhen2 to; explore unique features, monitor dynamics, and analyze the functional impact of non-synonymous single-nucleotide polymorphisms of the six NagA of most ruinous Mycobacterium species; tuberculosis (Mtb), smegmatis (MS), marinum (MM), ulcerans, africanum, and microti respectively. This approach is essential for multi-targeting and could result in the identification of potential polypharmacological antitubercular compounds. Comparative sequential analyses revealed ≤ 50% of the overall structure, including the catalytic Asp267 and reactive Cys131, remained conserved. Interestingly, MS-NagA and MM-NagA possess unique hydrophobic isoleucine (Ile) residues at their active sites in contrast to leucine (Leu) found in other variants. More so, unique to the active sites of the NagA is a 'subunit loop' that covers the active site; probably crucial in binding (entry and exit) mechanisms of targeted NagA inhibitors. Relatively, nsSNP mutations exerted a destabilizing effect on the native NagA conformation. Structural and dynamical insights provided, basically pin-pointed the "Achilles' heel" explorable for the rational drug design of target-specific 'NagA' inhibitors potent against a wide range of mycobacterial diseases.
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Affiliation(s)
- Adeniyi T Adewumi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Pritika Ramharack
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Opeyemi S Soremekun
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
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Merikanto I, Laakso JT, Kaitala V. Outside-host phage therapy as a biological control against environmental infectious diseases. Theor Biol Med Model 2018; 15:7. [PMID: 29879998 PMCID: PMC5992827 DOI: 10.1186/s12976-018-0079-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/09/2018] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Environmentally growing pathogens present an increasing threat for human health, wildlife and food production. Treating the hosts with antibiotics or parasitic bacteriophages fail to eliminate diseases that grow also in the outside-host environment. However, bacteriophages could be utilized to suppress the pathogen population sizes in the outside-host environment in order to prevent disease outbreaks. Here, we introduce a novel epidemiological model to assess how the phage infections of the bacterial pathogens affect epidemiological dynamics of the environmentally growing pathogens. We assess whether the phage therapy in the outside-host environment could be utilized as a biological control method against these diseases. We also consider how phage-resistant competitors affect the outcome, a common problem in phage therapy. The models give predictions for the scenarios where the outside-host phage therapy will work and where it will fail to control the disease. Parameterization of the model is based on the fish columnaris disease that causes significant economic losses to aquaculture worldwide. However, the model is also suitable for other environmentally growing bacterial diseases. RESULTS Transmission rates of the phage determine the success of infectious disease control, with high-transmission phage enabling the recovery of the host population that would in the absence of the phage go asymptotically extinct due to the disease. In the presence of outside-host bacterial competition between the pathogen and phage-resistant strain, the trade-off between the pathogen infectivity and the phage resistance determines phage therapy outcome from stable coexistence to local host extinction. CONCLUSIONS We propose that the success of phage therapy strongly depends on the underlying biology, such as the strength of trade-off between the pathogen infectivity and the phage-resistance, as well as on the rate that the phages infect the bacteria. Our results indicate that phage therapy can fail if there are phage-resistant bacteria and the trade-off between pathogen infectivity and phage resistance does not completely inhibit the pathogen infectivity. Also, the rate that the phages infect the bacteria should be sufficiently high for phage-therapy to succeed.
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Affiliation(s)
- Ilona Merikanto
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
- Department of Psychology and logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- National Institute for Health and Welfare, Helsinki, Finland.
| | - Jouni T Laakso
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Centre of Excellence in Biological Interactions, University of Jyväskylä, Jyväskylä, Finland
| | - Veijo Kaitala
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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Mononen T, Ruokolainen L. Spatial disease dynamics of free-living pathogens under pathogen predation. Sci Rep 2017; 7:7729. [PMID: 28798313 PMCID: PMC5552698 DOI: 10.1038/s41598-017-07983-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/03/2017] [Indexed: 11/09/2022] Open
Abstract
The epidemiological dynamics of potentially free-living pathogens are often studied with respect to a specific pathogen species (e.g., cholera) and most studies concentrate only on host-pathogen interactions. Here we show that metacommunity-level interactions can alter conventional spatial disease dynamics. We introduce a pathogen eating consumer species and investigate a deterministic epidemiological model of two habitat patches, where both patches can be occupied by hosts, pathogens, and consumers of free-living pathogens. An isolated habitat patch shows periodic disease outbreaks in the host population, arising from cyclic consumer-pathogen dynamics. On the other hand, consumer dispersal between the patches generate asymmetric disease prevalence, such that the host population in one patch stays disease-free, while disease outbreaks occur in the other patch. Such asymmetry can also arise with host dispersal, where infected hosts carry pathogens to the other patch. This indirect movement of pathogens causes also a counter-intuitive effect: decreasing morbidity in a focal patch under increasing pathogen immigration. Our results underline that community-level interactions influence disease dynamics and consistent spatial asymmetry can arise also in spatially homogeneous systems.
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Affiliation(s)
- Tommi Mononen
- University of Helsinki, Department of Biosciences, Helsinki, FI-00014, Finland.
| | - Lasse Ruokolainen
- University of Helsinki, Department of Biosciences, Helsinki, FI-00014, Finland
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Merikanto I, Laakso JT, Kaitala V. Outside-host predation as a biological control against an environmental opportunist disease. Ecol Modell 2017. [DOI: 10.1016/j.ecolmodel.2017.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Legrand J, Bolotin-Fukuhara M, Bourgais A, Fairhead C, Sicard D. Life-history strategies and carbon metabolism gene dosage in the Nakaseomyces yeasts. FEMS Yeast Res 2015; 16:fov112. [PMID: 26684721 DOI: 10.1093/femsyr/fov112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2015] [Indexed: 12/14/2022] Open
Abstract
The Nakaseomyces clade consists of a group of six hemiascomyceteous yeasts (Candida glabrata, Nakaseomyces delphensis, C. nivarensis, C. bracarensis, C. castelli, N. bacillisporus), phylogenetically close to the yeast Saccharomyces cerevisiae, their representative being the well-known pathogenic yeast C. glabrata. Four species had been previously examined for their carbon assimilation properties and found to have similar properties to S. cerevisiae (repression of respiration in high glucose-i.e. Crabtree positivity-and being a facultative anaerobe). We examined here the complete set of the six species for their carbon metabolic gene content. We also measured different metabolic and life-history traits (glucose consumption rate, population growth rate, carrying capacity, cell size, cell and biomass yield). We observed deviations from the glycolytic gene redundancy observed in S. cerevisiae presumed to be an important property for the Crabtree positivity, especially for the two species C. castelli and N. bacillisporus which frequently have only one gene copy, but different life strategies. Therefore, we show that the decrease in carbon metabolic gene copy cannot be simply associated with a reduction of glucose consumption rate and can be counterbalanced by other beneficial genetic variations.
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Affiliation(s)
- Judith Legrand
- Univ Paris-Sud, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Monique Bolotin-Fukuhara
- CNRS UMR 8621 Institut de Génétique et Microbiologie, Univ Paris Sud F-91140 Orsay Cedex CNRS, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Aurélie Bourgais
- Univ Paris-Sud, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Cécile Fairhead
- CNRS UMR 8621 Institut de Génétique et Microbiologie, Univ Paris Sud F-91140 Orsay Cedex CNRS, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Delphine Sicard
- Univ Paris-Sud, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France INRA, UMR 1083 Sciences pour l'oenologie, 34060 Montpellier Cedex 2, France
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