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Wang Y, Wang Z, Ali A, Su J, Huang T, Hou C, Li X. Microbial-induced calcium precipitation: Bibliometric analysis, reaction mechanisms, mineralization types, and perspectives. CHEMOSPHERE 2024; 362:142762. [PMID: 38971440 DOI: 10.1016/j.chemosphere.2024.142762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 06/27/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Microbial-induced calcium precipitation (MICP) refers to the formation of calcium precipitates induced by mineralization during microbial metabolism. MICP has been widely used as an ecologically sustainable method in environmental, geotechnical, and construction fields. This article reviews the removal mechanisms of MICP for different contaminants in the field of water treatment. The nucleation pathway is explained at both extracellular and intracellular levels, with a focus on evaluating the contribution of extracellular polymers to MICP. The types of mineralization and the regulatory role of enzyme genes in the MICP process are innovatively summarized. Based on this, the environmental significance of MICP is illustrated, and the application prospects of calcium precipitation products are discussed. The research hotspots and development trends of MICP are analyzed by bibliometric methods, and the challenges and future directions of MICP technology are identified. This review aims to provide a theoretical basis for further understanding of the MICP phenomenon in water treatment and the effective removal of multiple pollutants, which will help researchers to find the breakthroughs and innovations in the existing technologies, with a view to making significant progress in MICP technology.
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Affiliation(s)
- Yuxuan Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Zhao Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Amjad Ali
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Junfeng Su
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Tinglin Huang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Chenxi Hou
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Xuan Li
- College of Environmental Science & Engineering, Yancheng Institute of Technology, Yancheng, 224051, China
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Chen H, Zheng H, Cai C, Wang H, Gai C, Tan Z, Dai H, Mei W. New indole derivatives from endophytic fungus Colletotruchum sp. HK-08 originated from leaves of Nerium indicum. CHINESE HERBAL MEDICINES 2024; 16:235-238. [PMID: 38706824 PMCID: PMC11064624 DOI: 10.1016/j.chmed.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/24/2023] [Accepted: 07/18/2023] [Indexed: 05/07/2024] Open
Abstract
Objective To study secondary metabolites from endophytic fungus Colletotruchum sp. HK-08 originated from the leaves of Nerium indicum. Methods The compounds were isolated by various column chromatographic techniques, and their structures were elucidated by spectroscopic techniques [high resolution electrospray ionization mass spectroscopy (HRESIMS), one-dimensional (1D) and two-dimensional (2D) nuclear magnetic resonance spectroscopy (NMR)], as well as comparison with literature data. The Ellman method was used to determine the acetylcholinesterase (AChE) inhibitory activity. Results Four indole derivatives were identified from Colletotruchum sp. HK-08, including 6'-hydroxymonaspiloindole (1), 2-(2-oxoindolin-3-yl)ethyl 2-(4-hydroxyphenyl) acetate (2), 2-(2-oxoindolin-3-yl)ethyl 2-(2-hydroxyphenyl)acetate (3), and monaspiloindole (4). Compound 4 presented weak AChE inhibitory activity with IC50 value of (69.30 ± 6.27) μmol/L [tacrine as the positive control, with IC50 value of (0.61 ± 0.07) μmol/L]. Conclusion Compounds 1-3 were new compounds, and compound 4 had weak AChE inhibitory activity.
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Affiliation(s)
- Huiqin Chen
- Hainan Key Laboratory of Research and Development of Natural Product from Li Folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| | - Hao Zheng
- Hainan Key Laboratory of Research and Development of Natural Product from Li Folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| | - Caihong Cai
- Hainan Key Laboratory of Research and Development of Natural Product from Li Folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| | - Hao Wang
- Hainan Key Laboratory of Research and Development of Natural Product from Li Folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| | - Cuijuan Gai
- Hainan Key Laboratory of Research and Development of Natural Product from Li Folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| | - Zhiqiong Tan
- School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Haofu Dai
- Hainan Key Laboratory of Research and Development of Natural Product from Li Folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| | - Wenli Mei
- Hainan Key Laboratory of Research and Development of Natural Product from Li Folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
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Decadt H, Vermote L, Díaz-Muñoz C, Weckx S, De Vuyst L. Decarboxylase activity of the non-starter lactic acid bacterium Loigolactobacillus rennini gives crack defects in Gouda cheese through the production of γ-aminobutyric acid. Appl Environ Microbiol 2024; 90:e0165523. [PMID: 38231565 PMCID: PMC10880667 DOI: 10.1128/aem.01655-23] [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: 09/18/2023] [Accepted: 11/29/2023] [Indexed: 01/18/2024] Open
Abstract
Ten Gouda cheese wheels with an age of 31 weeks from six different batch productions were affected by a crack defect and displayed an unpleasant off-flavor. To unravel the causes of these defects, the concentrations of free amino acids, other organic acids, volatile organic compounds, and biogenic amines were quantified in zones around the cracks and in zones without cracks, and compared with those of similar Gouda cheeses without crack defect. The Gouda cheeses with cracks had a significantly different metabolome. The production of the non-proteinogenic amino acid γ-aminobutyric acid (GABA) could be unraveled as the key mechanism leading to crack formation, although the production of the biogenic amines cadaverine and putrescine contributed as well. High-throughput amplicon sequencing of the full-length 16S rRNA gene based on whole-community DNA revealed the presence of Loigolactobacillus rennini and Tetragenococcus halophilus as most abundant non-starter lactic acid bacteria in the zones with cracks. Shotgun metagenomic sequencing allowed to obtain a metagenome-assembled genome of both Loil. rennini and T. halophilus. However, only Loil. rennini contained genes necessary for the production of GABA, cadaverine, and putrescine. Metagenetics further revealed the brine and the rennet used during cheese manufacturing as the most plausible inoculation sources of both Loil. rennini and T. halophilus.IMPORTANCECrack defects in Gouda cheeses are still poorly understood, although they can lead to major economic losses in cheese companies. In this study, the bacterial cause of a crack defect in Gouda cheeses was identified, and the pathways involved in the crack formation were unraveled. Moreover, possible contamination sources were identified. The brine bath might be a major source of bacteria with the potential to deteriorate cheese quality, which suggests that cheese producers should regularly investigate the quality and microbial composition of their brines. This study illustrated how a multiphasic approach can understand and mitigate problems in a cheese company.
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Affiliation(s)
- Hannes Decadt
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Louise Vermote
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Cristian Díaz-Muñoz
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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Ritschard JS, Schuppler M. The Microbial Diversity on the Surface of Smear-Ripened Cheeses and Its Impact on Cheese Quality and Safety. Foods 2024; 13:214. [PMID: 38254515 PMCID: PMC10814198 DOI: 10.3390/foods13020214] [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: 12/07/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Smear-ripened cheeses are characterized by a viscous, red-orange surface smear on their rind. It is the complex surface microbiota on the cheese rind that is responsible for the characteristic appearance of this cheese type, but also for the wide range of flavors and textures of the many varieties of smear-ripened cheeses. The surface smear microbiota also represents an important line of defense against the colonization with undesirable microorganisms through various types of interaction, such as competitive exclusion or production of antimicrobial substances. Predominant members of the surface smear microbiota are salt-tolerant yeast and bacteria of the phyla Actinobacteria, Firmicutes, and Proteobacteria. In the past, classical culture-based approaches already shed light on the composition and succession of microorganisms and their individual contribution to the typicity of this cheese type. However, during the last decade, the introduction and application of novel molecular approaches with high-resolution power provided further in-depth analysis and, thus, a much more detailed view of the composition, structure, and diversity of the cheese smear microbiota. This led to abundant novel knowledge, such as the identification of so far unknown community members. Hence, this review is summarizing the current knowledge of the diversity of the surface smear microbiota and its contribution to the quality and safety of smear-ripened cheese. If the succession or composition of the surface-smear microbiota is disturbed, cheese smear defects might occur, which may promote food safety issues. Hence, the discussion of cheese smear defects in the context of an increased understanding of the intricate surface smear ecosystem in this review may not only help in troubleshooting and quality control but also paves the way for innovations that can lead to safer, more consistent, and higher-quality smear-ripened cheeses.
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Affiliation(s)
| | - Markus Schuppler
- Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland;
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5
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Mills S, Trego AC, Prevedello M, De Vrieze J, O’Flaherty V, Lens PN, Collins G. Unifying concepts in methanogenic, aerobic, and anammox sludge granulation. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 17:100310. [PMID: 37705860 PMCID: PMC10495608 DOI: 10.1016/j.ese.2023.100310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 06/17/2023] [Accepted: 08/05/2023] [Indexed: 09/15/2023]
Abstract
The retention of dense and well-functioning microbial biomass is crucial for effective pollutant removal in several biological wastewater treatment technologies. High solids retention is often achieved through aggregation of microbial communities into dense, spherical aggregates known as granules, which were initially discovered in the 1980s. These granules have since been widely applied in upflow anaerobic digesters for waste-to-energy conversions. Furthermore, granular biomass has been applied in aerobic wastewater treatment and anaerobic ammonium oxidation (anammox) technologies. The mechanisms underpinning the formation of methanogenic, aerobic, and anammox granules are the subject of ongoing research. Although each granule type has been extensively studied in isolation, there has been a lack of comparative studies among these granulation processes. It is likely that there are some unifying concepts that are shared by all three sludge types. Identifying these unifying concepts could allow a unified theory of granulation to be formed. Here, we review the granulation mechanisms of methanogenic, aerobic, and anammox granular sludge, highlighting several common concepts, such as the role of extracellular polymeric substances, cations, and operational parameters like upflow velocity and shear force. We have then identified some unique features of each granule type, such as different internal structures, microbial compositions, and quorum sensing systems. Finally, we propose that future research should prioritize aspects of microbial ecology, such as community assembly or interspecies interactions in individual granules during their formation and growth.
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Affiliation(s)
- Simon Mills
- Microbial Communities Laboratory, School of Biological and Chemical Sciences, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Anna Christine Trego
- Microbial Ecology Laboratory School of Biological and Chemical Sciences, University of Galway, University Road, Galway, H91 TK33, Ireland
| | - Marco Prevedello
- Microbial Communities Laboratory, School of Biological and Chemical Sciences, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Vincent O’Flaherty
- Microbial Ecology Laboratory School of Biological and Chemical Sciences, University of Galway, University Road, Galway, H91 TK33, Ireland
| | - Piet N.L. Lens
- University of Galway, University Road, Galway, H91 TK33, Ireland
| | - Gavin Collins
- Microbial Communities Laboratory, School of Biological and Chemical Sciences, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
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Camacho Silvas LA. [Bacterial resistance, a current crisis.]. Rev Esp Salud Publica 2023; 97:e202302013. [PMID: 36815211 PMCID: PMC10541255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 02/06/2023] [Indexed: 02/24/2023] Open
Abstract
Bacterial resistance is a constant battle representing a Public Health trouble. So much, that the World Health Organization considerate Public Health as a priority in health, due to the impact that generates as much as in health (giving that recent projections indicate that by 2050 it'll be produced more deaths because of this than the ones occasioned because of cancer) as its economic impact (which, according to a recent study in the United Kingdom, it'll cost the world's economy an estimated of 100 trillion dollars). The quick appearance of multidrug-resistant and pandrug-resistant bacteria is a world nature phenomenon, questioning the antibiotics efficiency. Implement protocols and recommendations is essential, just as essential and necessary as give awareness to health personnel, taking as base the knowledge of resistance generation and its impact through the years, empowered by the actual pandemic of COVID 19.
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Affiliation(s)
- Luis Arturo Camacho Silvas
- Laboratorio de Farmacoepidemiología, Facultad de Medicina y Ciencias Biomédicas, Universidad Autónoma de ChihuahuaUniversidad Autónoma de ChihuahuaChihuahuaMexico
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Reuben RC, Langer D, Eisenhauer N, Jurburg SD. Universal drivers of cheese microbiomes. iScience 2023; 26:105744. [PMID: 36582819 PMCID: PMC9792889 DOI: 10.1016/j.isci.2022.105744] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/25/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
The culinary value, quality, and safety of cheese are largely driven by the resident bacteria, but comparative analyses of the cheese microbiota across cheese types are scarce. We present the first global synthesis of cheese microbiomes. Following a systematic literature review of cheese microbiology research, we collected 16S rRNA gene amplicon sequence data from 824 cheese samples spanning 58 cheese types and 16 countries. We found a consistent, positive relationship between microbiome richness and pH, and a higher microbial richness in cheeses derived from goat milk. In contrast, we found no relationship between pasteurization, geographic location, or salinity and richness. Milk and cheese type, geographic location, and pasteurization collectively explained 65% of the variation in microbial community composition. Importantly, we identified four universal cheese microbiome types, driven by distinct dominant taxa. Our study reveals notable diversity patterns among the cheese microbiota, which are driven by geography and local environmental variables.
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Affiliation(s)
- Rine Christopher Reuben
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstraße 4, 04103 Leipzig, Germany
| | - Désirée Langer
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Nico Eisenhauer
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstraße 4, 04103 Leipzig, Germany
| | - Stephanie D. Jurburg
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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Nikbakht Brujeni G, Houshmand P, Soufizadeh P. Bovine leukemia virus: a perspective insight into the infection and immunity. IRANIAN JOURNAL OF VETERINARY RESEARCH 2023; 24:290-300. [PMID: 38799292 PMCID: PMC11127729 DOI: 10.22099/ijvr.2023.48236.7023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/30/2023] [Accepted: 10/21/2023] [Indexed: 05/29/2024]
Abstract
Bovine leukemia virus (BLV) is a member of the Retroviridae family and belongs to the Deltaretrovirus genus. It has a close relationship with human T-cell leukemia virus type I. BLV is responsible for causing enzootic bovine leukosis (EBL), a contagious disease that affects the bovine lymphatic system. This virus poses challenges for the global cattle industry, as it impacts cattle populations all over the world. Despite being widespread and impactful, BLV often goes unnoticed, with many researchers unaware of its presence and the potential consequences it carries. BLV demonstrates varying levels of pathogenicity. The majority of cattle (around 70%) become seropositive asymptomatic carriers, displaying no noticeable clinical symptoms. However, a smaller proportion of infected animals experience persistent lymphocytosis, characterized by an elevated number of lymphocytes in the bloodstream. If not monitored and managed, a subset of these persistently infected cattle may advance to lymphosarcoma. This condition typically presents as tumors in different lymphoid tissues, impacting various organs and overall health and productivity. Furthermore, recent research has highlighted the potential association between the occurrence of breast and lung cancer in humans and the presence of BLV. This review will delve into the recent discoveries concerning BLV, specifically exploring its epidemiology, the economic impact it has on the global cattle industry, its implications for human medicine, and the association between different alleles of the major histocompatibility complex (MHC) and susceptibility or resistance to BLV. Bovine leukemia virus, Enzootic bovine leukosis, Major histocompatibility complex, Retroviridae.
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Affiliation(s)
- Gh. Nikbakht Brujeni
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - P. Houshmand
- Ph.D. Student in Immunology, Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - P. Soufizadeh
- Graduated from Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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9
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Sidhu N, Goyal S, Reddy MS. Biomineralization of cyanobacteria Synechocystis pevalekii improves the durability properties of cement mortar. AMB Express 2022; 12:59. [PMID: 35587839 PMCID: PMC9120275 DOI: 10.1186/s13568-022-01403-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 05/11/2022] [Indexed: 11/21/2022] Open
Abstract
Microbially induced calcium carbonate precipitation (MICCP) is considered a novel eco-friendly technique to enhance the structural properties of cementitious-based material. Maximum studies have emphasized using ureolytic bacteria to improve the durability properties of building structures. In this study, the role of photoautotrophic bacteria Synechocystis pevalekii BDHKU 35101 has been investigated for calcium carbonate precipitation in sand consolidation, and enhancing mechanical and permeability properties of cement mortar. Both live and UV-treated S. pevalekii cells were used to treat the mortar specimens, and the results were compared with the control. The compressive strength of mortar specimens was significantly enhanced by 25.54% and 15.84% with live and UV-treated S. pevalekii cells at 28-day of curing. Water absorption levels were significantly reduced in bacterial-treated mortar specimens compared to control at 7 and 28-day curing. Calcium carbonate precipitation was higher in live-treated cells than in UV-treated S. pevalekii cells. Calcium carbonate precipitation by S. pevalekii cells was confirmed with SEM-EDS, XRD, and TGA analysis. These results suggest that S. pevalekii can serve as a low-cost and environment friendly MICCP technology to improve the durability properties of cementitious materials. Cyanobacterial Synechocystis pevalekii cells induced calcification on cement mortar. Both live and UV-treated cells increased the compressive strength and reduced the water absorption. Biomineralization by S. pevalekii serves as a low-cost and eco-friendly MICCP technology.
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Mutungwazi A, Ijoma GN, Ogola HJO, Matambo TS. Physico-Chemical and Metagenomic Profile Analyses of Animal Manures Routinely Used as Inocula in Anaerobic Digestion for Biogas Production. Microorganisms 2022; 10:671. [PMID: 35456722 PMCID: PMC9033126 DOI: 10.3390/microorganisms10040671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 02/05/2023] Open
Abstract
Anaerobic digestion (AD) of organic waste is considered a sustainable solution to energy shortage and waste management challenges. The process is facilitated by complex communities of micro-organisms, yet most wastes do not have these and thus need microbial inoculation using animal manures to initiate the process. However, the degradation efficiency and methane yield achieved in using different inocula vary due to their different microbial diversities. This study used metagenomics tools to compare the autochthonous microbial composition of cow, pig, chicken, and horse manures commonly used for biogas production. Cows exhibited the highest carbon utilisation (>30%) and showed a carbon to nitrogen ratio (C/N) favourable for microbial growth. Pigs showed the least nitrogen utilisation (<3%) which explains their low C/N whilst horses showed the highest nitrogen utilisation (>40%), which explains its high C/N above the optimal range of 20−30 for efficient AD. Manures from animals with similar gastrointestinal tract (GIT) physiologies were observed to largely harbour similar microbial communities. Conversely, some samples from animals with different GITs also shared common microbial communities plausibly because of similar diets and rearing conditions. Insights from this study will lay a foundation upon which in-depth studies of AD metabolic pathways and strategies to boost methane production through efficient catalysis can be derived.
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Affiliation(s)
- Asheal Mutungwazi
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa (UNISA), 28 Pioneer Ave, Cnr Christiaan De Wet & Pioneer Rds., Florida Park, Roodepoort, Johannesburg 1709, South Africa; (A.M.); (G.N.I.)
| | - Grace N. Ijoma
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa (UNISA), 28 Pioneer Ave, Cnr Christiaan De Wet & Pioneer Rds., Florida Park, Roodepoort, Johannesburg 1709, South Africa; (A.M.); (G.N.I.)
| | - Henry J. O. Ogola
- Centre for Research, Innovation and Technology, Jaramogi Oginga Odinga University of Science and Technology, Bondo P.O. Box 210-40601, Kenya;
| | - Tonderayi S. Matambo
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa (UNISA), 28 Pioneer Ave, Cnr Christiaan De Wet & Pioneer Rds., Florida Park, Roodepoort, Johannesburg 1709, South Africa; (A.M.); (G.N.I.)
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11
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Qu A, Zhang Y, Shi H, Wang H, Ding K, Pan ZH, Zhao G, Hadiatullah H. Investigation of gas-producing bacteria in sufu and its effective method to control their growth. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Jeong J, Mun S, Oh Y, Cho CS, Yun K, Ahn Y, Chung WH, Lim MY, Lee KE, Hwang TS, Han K. A qRT-PCR Method Capable of Quantifying Specific Microorganisms Compared to NGS-Based Metagenome Profiling Data. Microorganisms 2022; 10:microorganisms10020324. [PMID: 35208779 PMCID: PMC8875016 DOI: 10.3390/microorganisms10020324] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 01/25/2023] Open
Abstract
Metagenome profiling research using next-generation sequencing (NGS), a technique widely used to analyze the diversity and composition of microorganisms living in the human body, especially the gastrointestinal tract, has been actively conducted, and there is a growing interest in the quantitative and diagnostic technology for specific microorganisms. According to recent trends, quantitative real-time PCR (qRT-PCR) is still a considerable technique in detecting and quantifying bacteria associated with the human oral and nasal cavities, due to the analytical cost and time burden of NGS technology. Here, based on NGS metagenome profiling data produced by utilizing 100 gut microbiota samples, we conducted a comparative analysis for the identification and quantification of five bacterial genera (Akkermansia, Bacteroides, Bifidobacterium, Phascolarctobacterium, and Roseburia) within same metagenomic DNA samples through qRT-PCR assay in parallel. Genus-specific primers, targeting the particular gene of each genus for qRT-PCR assay, allowed a statistically consistent quantification pattern with the metagenome profiling data. Furthermore, results of bacterial identification through Sanger validation demonstrated the high genus-specificity of each primer set. Therefore, our study suggests that an approach to quantifying specific microorganisms by applying the qRT-PCR method can compensate for the concerns (potential issues) of NGS while also providing efficient benefits to various microbial industries.
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Affiliation(s)
- Jinuk Jeong
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea; (J.J.); (Y.O.)
| | - Seyoung Mun
- Department of Nanobiomedical Science, Dankook University, Cheonan 31116, Korea;
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
| | - Yunseok Oh
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea; (J.J.); (Y.O.)
| | - Chun-Sung Cho
- Department of Neurosurgery, College of Medicine, Dankook University, Cheonan 31116, Korea;
| | - Kyeongeui Yun
- HuNBiome Co., Ltd., Seoul 08507, Korea; (K.Y.); (Y.A.)
| | - Yongju Ahn
- HuNBiome Co., Ltd., Seoul 08507, Korea; (K.Y.); (Y.A.)
| | - Won-Hyong Chung
- Research Group of Healthcare, Korea Food Research Institute, Wanju 55365, Korea; (W.-H.C.); (M.Y.L.)
| | - Mi Young Lim
- Research Group of Healthcare, Korea Food Research Institute, Wanju 55365, Korea; (W.-H.C.); (M.Y.L.)
| | - Kyung Eun Lee
- Department of Oral Medicine, School of Dentistry, Jeonbuk National University, Jeonju 54896, Korea;
| | | | - Kyudong Han
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea; (J.J.); (Y.O.)
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- Correspondence: ; Tel.: +82-550-1240
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Tudu R, Banerjee J, Habib M, Bandyopadhyay S, Biswas S, Kesh SS, Maity A, Batabyal S, Polley S. Prevalence and molecular characterization of extended-spectrum β-lactamase (ESBL) producing Escherichia coli isolated from dogs suffering from diarrhea in and around Kolkata. IRANIAN JOURNAL OF VETERINARY RESEARCH 2022; 23:237-246. [PMID: 36425605 PMCID: PMC9681975 DOI: 10.22099/ijvr.2022.42543.6176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/21/2022] [Accepted: 05/02/2022] [Indexed: 03/17/2023]
Abstract
BACKGROUND Dogs are the favorite companion animals among humans. The close interaction between dogs and people increases the risk of antibiotic resistance spreading. Surveillance for antimicrobial resistance and the identification of ESBL-producing Escherichia coli as an indicator bacterium is an important tool for managing antimicrobial drug therapy. AIMS The present study targeted to identify and characterize ESBL-producing E. coli among dogs suffering from diarrhea in and around Kolkata. METHODS Isolation and identification of E. coli from dogs suffering from diarrhea (n=70) along with screening for the production of both ESBL and AmpC. The isolates were further characterized through antimicrobial resistance profiling, resistance genes (bla CTX-M, bla TEM, and bla SHV) screening, and phylogenetic group study. RESULTS Among the 70 isolates, 21 (30%) were confirmed ESBL producers. An antibiogram typing of ESBL-producing E. coli revealed that the majority of them were resistant to norfloxacin (85.7%) followed by tetracycline (61.90%), doxycycline (57.14%), piperacillin/tazobactam (52.38%), cotrimoxazole (47.62%), gentamicin (42.62%), amikacin (23.81%), and chloramphenicol (19.05%). Major resistance genes included bla CTX-M (100%), bla TEM (28.57%), and bla SHV (9.50%). The predominant phylogenetic groups were phylogroup A (76%) followed by phylogroup D (24%). CONCLUSION The current investigation reported a high prevalence of both ESBL and AmpC β-lactamase (AmpC) producing E. coli, co-resistance to a distinct group of antibiotics, and co-existence of different ESBL genes in dogs. Our findings highlight the importance of diagnostic antimicrobial susceptibility testing for proper antimicrobial therapy and to prevent antimicrobial resistance from spreading to humans from dogs in Kolkata and the surrounding area.
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Affiliation(s)
- R Tudu
- Department of Veterinary Biochemistry, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, 37, K. B. Sarani, Belgachia, Kolkata-700 037, West Bengal, India
| | - J Banerjee
- Ph.D. Student in Veterinary Biochemistry, Department of Veterinary Biochemistry, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, 37, K. B. Sarani, Belgachia, Kolkata-700 037, West Bengal, India
| | - Md Habib
- Ph.D. Student in Veterinary Biochemistry, Department of Veterinary Biochemistry, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, 37, K. B. Sarani, Belgachia, Kolkata-700 037, West Bengal, India
| | - S Bandyopadhyay
- Eastern Regional Station, Indian Veterinary Research Institute, Kolkata-700 037, West Bengal, India
| | - S Biswas
- Department of Veterinary Biochemistry, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, 37, K. B. Sarani, Belgachia, Kolkata-700 037, West Bengal, India
| | - S S Kesh
- Department of Veterinary Clinical Complex, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, 37, K. B. Sarani, Belgachia, Kolkata-700 037, West Bengal, India
| | - A Maity
- Department of Veterinary Biochemistry, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, 37, K. B. Sarani, Belgachia, Kolkata-700 037, West Bengal, India
| | - S Batabyal
- Department of Veterinary Biochemistry, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, 37, K. B. Sarani, Belgachia, Kolkata-700 037, West Bengal, India
| | - S Polley
- Department of Veterinary Biochemistry, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, 37, K. B. Sarani, Belgachia, Kolkata-700 037, West Bengal, India
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14
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Richter Ł, Paszkowska K, Cendrowska U, Olgiati F, Silva PJ, Gasbarri M, Guven ZP, Paczesny J, Stellacci F. Broad-spectrum nanoparticles against bacteriophage infections. NANOSCALE 2021; 13:18684-18694. [PMID: 34738613 PMCID: PMC8601202 DOI: 10.1039/d1nr04936d] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Viral infections caused by bacteriophages, i.e., viruses that kill bacteria are one of the most dangerous and common threats for bacteria-based bioreactors. More than 70% of biotechnology companies have admitted to encountering this problem. Despite phage infections being such a dangerous and widespread risk, there are no effective methods to avoid them to date. Herein, we present a novel technology based on nanoparticles that irreversibly deactivates bacteriophages and is safe for bacteria. Our method allows for the unsupervised protection of bacterial processes in the biotechnology industry. Gold nanoparticles coated with a mixture of negatively charged 11-mercapto 1-undecanesulfonic acid (MUS) and hydrophobic 1-octanethiol (OT) ligands are effective at deactivating various types of Escherichia coli-selective phages: T1, T4, and T7. The nanoparticles can lower the titer of phages up to 2 and 5 logs in 6 and 24 h at 50 °C, respectively. A comparative analysis of nanoparticles with different ligand shells illustrates the importance of the combination of negatively charged and hydrophobic ligands that is the key to achieving a good inhibitory concentration (EC50 ≤ 1 μg mL-1) for all tested phages. We show that the nanoparticles are harmless for the commonly used bacteria in industry Escherichia coli and are effective under conditions simulating the environment of bioreactors.
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Affiliation(s)
- Łukasz Richter
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Karolina Paszkowska
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Urszula Cendrowska
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Francesca Olgiati
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Paulo Jacob Silva
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Matteo Gasbarri
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Zekiye Pelin Guven
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Jan Paczesny
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Francesco Stellacci
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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Piqueras J, Chassard C, Callon C, Rifa E, Theil S, Lebecque A, Delbès C. Lactic Starter Dose Shapes S. aureus and STEC O26:H11 Growth, and Bacterial Community Patterns in Raw Milk Uncooked Pressed Cheeses. Microorganisms 2021; 9:microorganisms9051081. [PMID: 34069983 PMCID: PMC8157849 DOI: 10.3390/microorganisms9051081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 01/04/2023] Open
Abstract
Adding massive amounts of lactic starters to raw milk to manage the sanitary risk in the cheese-making process could be detrimental to microbial diversity. Adjusting the amount of the lactic starter used could be a key to manage these adverse impacts. In uncooked pressed cheeses, we investigated the impacts of varying the doses of a lactic starter (the recommended one, 1×, a 0.1× lower and a 2× higher) on acidification, growth of Staphylococcus aureus SA15 and Shiga-toxin-producing Escherichia coli (STEC) O26:H11 F43368, as well as on the bacterial community patterns. We observed a delayed acidification and an increase in the levels of pathogens with the 0.1× dose. This dose was associated with increased richness and evenness of cheese bacterial community and higher relative abundance of potential opportunistic bacteria or desirable species involved in cheese production. No effect of the increased lactic starter dose was observed. Given that sanitary criteria were paramount to our study, the increase in the pathogen levels observed at the 0.1× dose justified proscribing such a reduction in the tested cheese-making process. Despite this, the effects of adjusting the lactic starter dose on the balance of microbial populations of potential interest for cheese production deserve an in-depth evaluation.
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Affiliation(s)
- Justine Piqueras
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
| | - Christophe Chassard
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
| | - Cécile Callon
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
| | - Etienne Rifa
- UMR INSA/INRA 792, Toulouse Biotechnology Institute, INSA/CNRS 5504, 135 Avenue de Rangueil, F-31077 Toulouse, France;
| | - Sébastien Theil
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
| | - Annick Lebecque
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
| | - Céline Delbès
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
- Correspondence: ; Tel.: +33-471-456-419
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Rajasekar A, Wilkinson S, Moy CK. MICP as a potential sustainable technique to treat or entrap contaminants in the natural environment: A review. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2021; 6:100096. [PMID: 36159179 PMCID: PMC9488051 DOI: 10.1016/j.ese.2021.100096] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 05/25/2023]
Abstract
In the last two decades, developments in the area of biomineralization has yielded promising results making it a potentially environmentally friendly technique for a wide range of applications in engineering and wastewater/heavy metal remediation. Microbially Induced Carbonate Precipitation (MICP) has led to numerous patented applications ranging from novel strains and nutrient sources for the precipitation of biominerals. Studies are being constantly published to optimize the process to become a promising, cost effective, ecofriendly approach when compared with the existing traditional remediation technologies which are implemented to solve multiple contamination/pollution issues. Heavy metal pollution still poses a major threat towards compromising the ecosystem. The removal of heavy metals is of high importance due to their recalcitrance and persistence in the environment. In that perspective, this paper reviews the current and most significant discoveries and applications of MICP towards the conversion of heavy metals into heavy metal carbonates and removal of calcium from contaminated media such as polluted water. It is evident from the literature survey that although heavy metal carbonate research is very effective in removal, is still in its early stages but could serve as a solution if the microorganisms are stimulated directly in the heavy metal environment.
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Affiliation(s)
- Adharsh Rajasekar
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CIC-AEET), Nanjing University of Information Science &Technology, Nanjing, 210044, China
| | - Stephen Wilkinson
- Department of Civil Engineering, University of Wollongong in Dubai, Dubai, United Arab Emirates
| | - Charles K.S. Moy
- Department of Civil Engineering, Xi'an Jiaotong Liverpool University, Suzhou, Jiangsu, China
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17
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Xue Z, Brooks JT, Quart Z, Stevens ET, Kable ME, Heidenreich J, McLeod J, Marco ML. Microbiota Assessments for the Identification and Confirmation of Slit Defect-Causing Bacteria in Milk and Cheddar Cheese. mSystems 2021; 6:e01114-20. [PMID: 33563789 PMCID: PMC7883541 DOI: 10.1128/msystems.01114-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/16/2021] [Indexed: 01/04/2023] Open
Abstract
Validated methods are needed to detect spoilage microbes present in low numbers in foods and ingredients prior to defect onset. We applied propidium monoazide combined with 16S rRNA gene sequencing, qPCR, isolate identification, and pilot-scale cheese making to identify the microorganisms that cause slit defects in industrially produced Cheddar cheese. To investigate milk as the source of spoilage microbes, bacterial composition in milk was measured immediately before and after high-temperature, short-time (HTST) pasteurization over 10-h periods on 10 days and in the resulting cheese blocks. Besides HTST pasteurization-induced changes to milk microbiota composition, a significant increase in numbers of viable bacteria was observed over the 10-h run times of the pasteurizer, including 68-fold-higher numbers of the genus Thermus However, Thermus was not associated with slit development. Milk used to make cheese which developed slits instead contained a lower number of total bacteria, higher alpha diversity, and higher proportions of Lactobacillus, Bacillus, Brevibacillus, and Clostridium Only Lactobacillus proportions were significantly increased during cheese aging, and Limosilactobacillus (Lactobacillus) fermentum, in particular, was enriched in slit-containing cheeses and the pre- and post-HTST-pasteurization milk used to make them. Pilot-scale cheeses developed slits when inoculated with strains of L. fermentum, other heterofermentative lactic acid bacteria, or uncultured bacterial consortia from slit-associated pasteurized milk, thereby confirming that low-abundance taxa in milk can negatively affect cheese quality. The likelihood that certain microorganisms in milk cause slit defects can be predicted based on comparisons of the bacteria present in the milk used for cheese manufacture.IMPORTANCE Food production involves numerous control points for microorganisms to ensure quality and safety. These control points (e.g., pasteurization) are difficult to develop for fermented foods wherein some microbial contaminants are also expected to provide positive contributions to the final product and spoilage microbes may constitute only a small proportion of all microorganisms present. We showed that microbial composition assessments with 16S rRNA marker gene DNA sequencing are sufficiently robust to detect very-low-abundance bacterial taxa responsible for a major but sporadic Cheddar cheese spoilage defect. Bacterial composition in the (pasteurized) milk and cheese was associated with slit defect development. The application of Koch's postulates showed that individual bacterial isolates as well as uncultured bacterial consortia were sufficient to cause slits, even when present in very low numbers. This approach may be useful for detection and control of low-abundance spoilage microorganisms present in other foods.
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Affiliation(s)
- Zhengyao Xue
- Department of Food Science and Technology, University of California Davis, Davis, California, USA
- USDA, Agricultural Research Service, Western Human Nutrition Research Center, Immunity and Disease Prevention, Davis, California, USA
| | - Jason T Brooks
- Department of Food Science and Technology, University of California Davis, Davis, California, USA
| | - Zachary Quart
- Department of Food Science and Technology, University of California Davis, Davis, California, USA
| | - Eric T Stevens
- Department of Food Science and Technology, University of California Davis, Davis, California, USA
| | - Mary E Kable
- USDA, Agricultural Research Service, Western Human Nutrition Research Center, Immunity and Disease Prevention, Davis, California, USA
| | | | | | - Maria L Marco
- Department of Food Science and Technology, University of California Davis, Davis, California, USA
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18
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Wen S, Wang G, Yang Z, Wang Y, Rao M, Lu Q, Hong N. Next-Generation Sequencing Combined With Conventional Sanger Sequencing Reveals High Molecular Diversity in Actinidia Virus 1 Populations From Kiwifruit Grown in China. Front Microbiol 2020; 11:602039. [PMID: 33391218 PMCID: PMC7774462 DOI: 10.3389/fmicb.2020.602039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/11/2020] [Indexed: 01/04/2023] Open
Abstract
Kiwifruit (Actinidia spp.) is native to China. Viral disease–like symptoms are common on kiwifruit plants. In this study, six libraries prepared from total RNA of leaf samples from 69 kiwifruit plants were subjected to next-generation sequencing (NGS). Actinidia virus 1 (AcV-1), a tentative species in the family Closteroviridae, was discovered in the six libraries. Two full-length and two near-full genome sequences of AcV-1 variants were determined by Sanger sequencing. The genome structure of these Chinese AcV-1 variants was identical to that of isolate K75 and consisted of 12 open reading frames (ORFs). Analyses of these sequences together with the NGS-derived contig sequences revealed high molecular diversity in AcV-1 populations, with the highest sequence variation occurring at ORF1a, ORF2, and ORF3, and the available variants clustered into three phylogenetic clades. For the first time, our study revealed different domain compositions in the viral ORF1a and molecular recombination events among AcV-1 variants. Specific reverse transcriptase–polymerase chain reaction assays disclosed the presence of AcV-1 in plants of four kiwifruit species and unknown Actinidia spp. in seven provinces and one city.
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Affiliation(s)
- Shaohua Wen
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
| | - Guoping Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zuokun Yang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanxiang Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Min Rao
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qian Lu
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ni Hong
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
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Martelli F, Bancalari E, Neviani E, Bottari B. Novel insights on pink discoloration in cheese: The case of Pecorino Toscano. Int Dairy J 2020. [DOI: 10.1016/j.idairyj.2020.104829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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20
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Zheng Y, Chen J, Chen L, Hu T, Shi L, Wan S, Wang M. Analysis and control of microbial gas production in fermented chili paste. J FOOD PROCESS PRES 2020. [DOI: 10.1111/jfpp.14806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu Zheng
- State Key Laboratory of Food Nutrition and Safety Key Laboratory of Industrial Fermentation Microbiology Ministry of Education College of Biotechnology Tianjin University of Science and Technology Tianjin China
| | - Ju Chen
- State Key Laboratory of Food Nutrition and Safety Key Laboratory of Industrial Fermentation Microbiology Ministry of Education College of Biotechnology Tianjin University of Science and Technology Tianjin China
| | - Lin Chen
- State Key Laboratory of Food Nutrition and Safety Key Laboratory of Industrial Fermentation Microbiology Ministry of Education College of Biotechnology Tianjin University of Science and Technology Tianjin China
| | - Tao Hu
- State Key Laboratory of Food Nutrition and Safety Key Laboratory of Industrial Fermentation Microbiology Ministry of Education College of Biotechnology Tianjin University of Science and Technology Tianjin China
| | - Lei Shi
- Tianjin Limin Condiment Limited Company Tianjin China
| | - Shoupeng Wan
- Tianjin Limin Condiment Limited Company Tianjin China
| | - Min Wang
- State Key Laboratory of Food Nutrition and Safety Key Laboratory of Industrial Fermentation Microbiology Ministry of Education College of Biotechnology Tianjin University of Science and Technology Tianjin China
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21
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Ávila M, Gómez‐Torres N, Gaya P, Garde S. Effect of a nisin‐producing lactococcal starter on the late blowing defect of cheese caused by
Clostridium tyrobutyricum. Int J Food Sci Technol 2020. [DOI: 10.1111/ijfs.14598] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Marta Ávila
- Departamento de Tecnología de Alimentos Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Carretera de La Coruña km 7 28040 Madrid Spain
| | - Natalia Gómez‐Torres
- Departamento de Tecnología de Alimentos Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Carretera de La Coruña km 7 28040 Madrid Spain
| | - Pilar Gaya
- Departamento de Tecnología de Alimentos Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Carretera de La Coruña km 7 28040 Madrid Spain
| | - Sonia Garde
- Departamento de Tecnología de Alimentos Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Carretera de La Coruña km 7 28040 Madrid Spain
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Wokorach G, Otim G, Njuguna J, Edema H, Njung'e V, Machuka EM, Yao N, Stomeo F, Echodu R. Genomic analysis of Sweet potato feathery mottle virus from East Africa. PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY 2020; 110:101473. [PMID: 32454559 PMCID: PMC7233136 DOI: 10.1016/j.pmpp.2020.101473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 06/11/2023]
Abstract
Sweet potato feathery mottle virus is a potyvirus that infect sweet potato. The genome of the virus was analysed to understand genetic diversity, evolution and gene flow. Motifs, nucleotide identity and a phylogenetic tree were used to determine phylogroup of the isolates. Gene flow and genetic diversity were tested using DnaSP v.5. Codons evolution were tested using three methods embedded in Datamonkey. The results indicate occurrence of an isolate of phylogroup B within East Africa. Low genetic differentiation was observed between isolates from Kenya and Uganda indicating evidence of gene flow between the two countries. Four genes were found to have positively selected codons bordering or occurring within functional motifs. A motif within P1 gene evolved differently between phylogroup A and B. The evidence of gene flow indicates frequent exchange of the virus between the two countries and P1 gene motif provide a possible marker that can be used for mapping the distribution of the phylogroups.
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Affiliation(s)
- Godfrey Wokorach
- Biosciences Research Laboratory, Gulu University, P.O. Box 166, Gulu, Uganda
| | - Geoffrey Otim
- Biosciences Research Laboratory, Gulu University, P.O. Box 166, Gulu, Uganda
- Faculty of Agriculture, Gulu University, P.O. Box 166, Gulu, Uganda
| | - Joyce Njuguna
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Hilary Edema
- Biosciences Research Laboratory, Gulu University, P.O. Box 166, Gulu, Uganda
| | - Vincent Njung'e
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Eunice M. Machuka
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Nasser Yao
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Francesca Stomeo
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Richard Echodu
- Biosciences Research Laboratory, Gulu University, P.O. Box 166, Gulu, Uganda
- Faculty of Agriculture, Gulu University, P.O. Box 166, Gulu, Uganda
- Department of Biology, Faculty of Science, Gulu University, P.O. Box 166, Gulu, Uganda
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Analysis of the Bacterial Diversity of Paipa Cheese (a Traditional Raw Cow's Milk Cheese from Colombia) by High-Throughput Sequencing. Microorganisms 2020; 8:microorganisms8020218. [PMID: 32041151 PMCID: PMC7074763 DOI: 10.3390/microorganisms8020218] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 12/18/2022] Open
Abstract
Background: Paipa cheese is a traditional, semi-ripened cheese made from raw cow’s milk in Colombia. The aim of this work was to gain insights on the microbiota of Paipa cheese by using a culture-independent approach. Method: two batches of Paipa cheese from three formal producers were sampled during ripening for 28 days. Total DNA from the cheese samples was used to obtain 16S rRNA gene sequences by using Illumina technology. Results: Firmicutes was the main phylum found in the cheeses (relative abundances: 59.2–82.0%), followed by Proteobacteria, Actinobacteria and Bacteroidetes. Lactococcus was the main genus, but other lactic acid bacteria (Enterococcus, Leuconostoc and Streptococcus) were also detected. Stapylococcus was also relevant in some cheese samples. The most important Proteobacteria were Enterobacteriaceae, Aeromonadaceae and Moraxellaceae. Enterobacter and Enterobacteriaceae (others) were detected in all cheese samples. Serratia and Citrobacter were detected in some samples. Aeromonas and Acinetobacter were also relevant. Other minor genera detected were Marinomonas, Corynebacterium 1 and Chryseobacterium. The principal coordinates analysis suggested that there were producer-dependent differences in the microbiota of Paipa cheeses. Conclusions: lactic acid bacteria are the main bacterial group in Paipa cheeses. However, other bacterial groups, including spoilage bacteria, potentially toxin producers, and bacteria potentially pathogenic to humans and/or prone to carry antimicrobial resistance genes are also relevant in the cheeses.
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Niu C, Xue Y, Liu C, Zheng F, Wang J, Li Q. Identification of gas-forming spoilage bacteria in chili sauce and its control using nisin and salt. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2019.108658] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ben Maamar S, Hu J, Hartmann EM. Implications of indoor microbial ecology and evolution on antibiotic resistance. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2020; 30:1-15. [PMID: 31591493 PMCID: PMC8075925 DOI: 10.1038/s41370-019-0171-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/17/2019] [Accepted: 08/18/2019] [Indexed: 05/19/2023]
Abstract
The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built environment design and operation may counter-intuitively favor negative health outcomes, particularly with regard to antibiotic resistance. Indoor environments contain microbes from both human and non-human origins, providing a unique venue for microbial interactions, including horizontal gene transfer. Furthermore, stressors present in the built environment could favor the exchange of genetic material in general and the retention of antibiotic resistance genes in particular. Intrinsic and acquired antibiotic resistance both pose a potential threat to human health; these phenomena need to be considered and controlled separately. The presence of both environmental and human-associated microbes, along with their associated antibiotic resistance genes, in the face of stressors, including antimicrobial chemicals, creates a unique opportunity for the undesirable spread of antibiotic resistance. In this review, we summarize studies and findings related to various interactions between human-associated bacteria, environmental bacteria, and built environment conditions, and particularly their relation to antibiotic resistance, aiming to guide "healthy" building design.
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Affiliation(s)
- Sarah Ben Maamar
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Jinglin Hu
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA.
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Kamilari E, Tomazou M, Antoniades A, Tsaltas D. High Throughput Sequencing Technologies as a New Toolbox for Deep Analysis, Characterization and Potentially Authentication of Protection Designation of Origin Cheeses? INTERNATIONAL JOURNAL OF FOOD SCIENCE 2019; 2019:5837301. [PMID: 31886165 PMCID: PMC6925717 DOI: 10.1155/2019/5837301] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/08/2019] [Accepted: 09/28/2019] [Indexed: 12/17/2022]
Abstract
Protected Designation of Origin (PDO) labeling of cheeses has been established by the European Union (EU) as a quality policy that assures the authenticity of a cheese produced in a specific region by applying traditional production methods. However, currently used scientific methods for differentiating and establishing PDO are limited in terms of time, cost, accuracy and their ability to identify through quantifiable methods PDO fraud. Cheese microbiome is a dynamic community that progressively changes throughout ripening, contributing via its metabolism to unique qualitative and sensorial characteristics that differentiate each cheese. High Throughput Sequencing (HTS) methodologies have enabled the more precise identification of the microbial communities developed in fermented cheeses, characterization of their population dynamics during the cheese ripening process, as well as their contribution to the development of specific organoleptic and physio-chemical characteristics. Therefore, their application may provide an additional tool to identify the key microbial species that contribute to PDO cheeses unique sensorial characteristics and to assist to define their typicityin order to distinguish them from various fraudulent products. Additionally, they may assist the cheese-makers to better evaluate the quality, as well as the safety of their products. In this structured literature review indications are provided on the potential for defining PDO enabling differentiating factors based on distinguishable microbial communities shaped throughout the ripening procedures associated to cheese sensorial characteristics, as revealed through metagenomic and metatranscriptomic studies. Conclusively, HTS applications, even though still underexploited, have the potential to demonstrate how the cheese microbiome can affect the ripening process and sensorial characteristics formation via the catabolism of the available nutrients and interplay with other compounds of the matrix and/or production of microbial origin metabolites and thus their further quality enhancement.
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Affiliation(s)
- Elena Kamilari
- Cyprus University of Technology, Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus
| | | | | | - Dimitrios Tsaltas
- Cyprus University of Technology, Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus
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de Haro LA, Arellano SM, Novák O, Feil R, Dumón AD, Mattio MF, Tarkowská D, Llauger G, Strnad M, Lunn JE, Pearce S, Figueroa CM, del Vas M. Mal de Río Cuarto virus infection causes hormone imbalance and sugar accumulation in wheat leaves. BMC PLANT BIOLOGY 2019; 19:112. [PMID: 30902042 PMCID: PMC6431059 DOI: 10.1186/s12870-019-1709-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/11/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Mal de Río Cuarto virus (MRCV) infects several monocotyledonous species including maize and wheat. Infected plants show shortened internodes, partial sterility, increased tillering and reduced root length. To better understand the molecular basis of the plant-virus interactions leading to these symptoms, we combined RNA sequencing with metabolite and hormone measurements. RESULTS More than 3000 differentially accumulated transcripts (DATs) were detected in MRCV-infected wheat plants at 21 days post inoculation compared to mock-inoculated plants. Infected plants exhibited decreased levels of TaSWEET13 transcripts, which are involved in sucrose phloem loading. Soluble sugars, starch, trehalose 6-phosphate (Tre6P), and organic and amino acids were all higher in MRCV-infected plants. In addition, several transcripts related to plant hormone metabolism, transport and signalling were increased upon MRCV infection. Transcripts coding for GA20ox, D14, MAX2 and SMAX1-like proteins involved in gibberellin biosynthesis and strigolactone signalling, were reduced. Transcripts involved in jasmonic acid, ethylene and brassinosteroid biosynthesis, perception and signalling and in auxin transport were also altered. Hormone measurements showed that jasmonic acid, brassinosteroids, abscisic acid and indole-3-acetic acid were significantly higher in infected leaves. CONCLUSIONS Our results indicate that MRCV causes a profound hormonal imbalance that, together with alterations in sugar partitioning, could account for the symptoms observed in MRCV-infected plants.
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Affiliation(s)
| | - Sofía Maité Arellano
- Instituto de Biotecnología, CICVyA, INTA, CONICET, Hurlingham, Buenos Aires Argentina
| | - Ondrej Novák
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany Czech Academy of Sciences, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | | | - Danuše Tarkowská
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany Czech Academy of Sciences, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Gabriela Llauger
- Instituto de Biotecnología, CICVyA, INTA, CONICET, Hurlingham, Buenos Aires Argentina
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany Czech Academy of Sciences, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - John Edward Lunn
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO USA
| | | | - Mariana del Vas
- Instituto de Biotecnología, CICVyA, INTA, CONICET, Hurlingham, Buenos Aires Argentina
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Ritschard JS, Amato L, Kumar Y, Müller B, Meile L, Schuppler M. The role of the surface smear microbiome in the development of defective smear on surface-ripened red-smear cheese. AIMS Microbiol 2018; 4:622-641. [PMID: 31294238 PMCID: PMC6613336 DOI: 10.3934/microbiol.2018.4.622] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/20/2018] [Indexed: 01/05/2023] Open
Abstract
The complex smear microbiota colonizing the surface of red-smear cheese fundamentally impacts the ripening process, appearance and shelf life of cheese. To decipher the prokaryotic composition of the cheese smear microbiome, the surface of a semi-hard surface ripened cheese was studied post-ripening by culture-based and culture-independent molecular approaches. The aim was to detect potential bacterial alterations in the composition of the cheese smear microbiota resulting from cheese storage in vacuum film-prepackaging, which is often accompanied by the development of a surface smear defect. Next-generation sequencing of amplified 16S rRNA gene fragments revealed an unexpected high diversity of a total of 132 different genera from the domains Bacteria and Archaea on the cheese surface. Beside typical smear organisms, our study revealed the presence of several microorganisms so far not associated with cheese, but related to milk, farm and cheese dairy environments. A 16S ribosomal RNA based analysis from total RNA identified the major metabolically active populations in the cheese surface smear as Actinobacteria of the genera Corynebacterium, Brevibacterium, Brachybacterium and Agrococcus. Comparison of data on a higher phylogenetic level revealed distinct differences in the composition of the cheese smear microbiome from the different samples. While the proportions of Proteobacteria and Bacteroidetes were increased in the smear of prepacked samples and in particular in defective smear, staphylococci showed an opposite trend and turned out to be strongly decreased in defective smear. In conclusion, next-generation sequencing of amplified 16S rRNA genes and 16S rRNA from total RNA extracts provided a much deeper insight into the bacterial composition of the cheese smear microbiota. The observed shifts in the microbial composition of samples from defect surface smear suggest that certain members of the Proteobacteria contribute to the observed negative organoleptic properties of the surface smear of cheese after prepacking in plastic foil.
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Affiliation(s)
- Jasmine S Ritschard
- Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Lea Amato
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Yadhu Kumar
- Eurofins GATC Biotech AG, Jakob-Stadler-Platz 7, 78467 Konstanz, Germany
| | - Britta Müller
- Eurofins GATC Biotech AG, Jakob-Stadler-Platz 7, 78467 Konstanz, Germany
| | - Leo Meile
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Markus Schuppler
- Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
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Gillman PK. A reassessment of the safety profile of monoamine oxidase inhibitors: elucidating tired old tyramine myths. J Neural Transm (Vienna) 2018; 125:1707-1717. [PMID: 30255284 DOI: 10.1007/s00702-018-1932-y] [Citation(s) in RCA: 191] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/17/2018] [Indexed: 01/24/2023]
Abstract
This review appraises over 150 recent original papers reporting data that demonstrate the greatly reduced tyramine content of modern-day 'foods', about which the medical literature has a paucity of information. It discusses the cardiovascular pharmacology of tyramine and the characteristics, extent, risks, and treatment of the blood pressure increases that sometimes result from tyramine ingestion (the pressor response). In past decades, cheese was the only food associated with documented fatalities resulting from hypertension. Today, few foods contain problematically high tyramine levels, which is a result of changes in international food production techniques (especially the use of starter cultures), and hygiene regulations. Nowadays, even 'matured' cheeses are usually safe in healthy-sized portions. The mechanism by which tyramine may be produced in foods (by certain micro-organisms) is explained and hundreds of recent estimations of cheeses are reviewed. Numerous other previously inadequately documented foods are reviewed, including fish and soy sauces, salami-type sausages, dried meats, beers, wines, and various condiments. Evidence that the risk of harm from the pressor response has previously been overstated is reviewed, and the iatrogenic harms from hasty and aggressive treatment of hypertensive urgency are re-evaluated. Evidence now suggests that MAOIs are of comparable safety to many newer drugs and are straightforward to use. Previously held concerns about MAOIs are misplaced and some are of over-estimated consequence. The variability of pressor sensitivity to tyramine between individuals means that the knowledge and judgement of doctors, and some care, are still required.
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Haastrup MK, Johansen P, Malskær AH, Castro-Mejía JL, Kot W, Krych L, Arneborg N, Jespersen L. Cheese brines from Danish dairies reveal a complex microbiota comprising several halotolerant bacteria and yeasts. Int J Food Microbiol 2018; 285:173-187. [PMID: 30176565 DOI: 10.1016/j.ijfoodmicro.2018.08.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/06/2018] [Accepted: 08/15/2018] [Indexed: 11/19/2022]
Abstract
The Danish Danbo cheese is a surface ripened semi-hard cheese, which before ripening is submerged in brine for up to 24 h. The brining is required in order to obtain the structural and organoleptic properties of the cheeses. Likewise, the content of NaCl in the cheese will influence especially the surface microbiota being of significant importance for flavour development and prevention of microbial spoilage. Even though the microbiota on cheese surfaces have been studied extensively, limited knowledge is available on the occurrence of microorganisms in cheese brine. The aim of the present study was to investigate by both culture-dependent and -independent techniques the brine microbiota in four Danish dairies producing Danbo cheese. The pH of the brines varied from 5.1 to 5.6 with a dry matter content from 20 to 27% (w/w). The content of lactate varied from 4.1 to 10.8 g/L and free amino acids from 65 to 224 mg/L. Bacteria were isolated on five different media with NaCl contents of 0.85-23.0% (w/v) NaCl. The highest count of 6.3 log CFU/mL was obtained on TSA added 4% (w/v) NaCl. For yeasts, the highest count was 3.7 log CFU/mL on MYGP added 8% (w/v) NaCl. A total of 31 bacterial and eight eukaryotic species were isolated including several halotolerant and/or halophilic species. Among bacteria, counts of ≥6.0 log CFU/mL were obtained for Tetragenococcus muriaticus and Psychrobacter celer, while counts between ≥4.5 and < 6.0 log CFU/mL were obtained for Lactococcus lactis, Staphylococcus equorum, Staphylococcus hominis, Chromohalobacter beijerinckii, Chromohalobacter japonicus and Microbacterium maritypicum. Among yeasts, counts of ≥3.5 log CFU/mL were only obtained for Debaryomyces hansenii. By amplicon-based high-throughput sequencing of 16S rRNA gene and ITS2 regions for bacteria and eukaryotes respectively, brines from the same dairy clustered together indicating the uniqueness of the dairy brine microbiota. To a great extent the results obtained by amplicon sequencing fitted with the culture-dependent technique though each of the two methodologies identified unique genera/species. Dairy brine handling procedures as e.g. microfiltration were found to influence the brine microbiota. The current study proves the occurrence of a specific dairy brine microbiota including several halotolerant and/or halophilic species most likely of sea salt origin. The importance of these species during especially the initial stages of cheese ripening and their influence on cheese quality and safety need to be investigated. Likewise, optimised brine handling procedures and microbial cultures are required to ensure an optimal brine microbiota.
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Affiliation(s)
- Martin Kragelund Haastrup
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Pernille Johansen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Agnete Harboe Malskær
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Josué L Castro-Mejía
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Witold Kot
- Environmental Microbiology and Biotechnology, University of Aarhus, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
| | - Lukasz Krych
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Nils Arneborg
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Lene Jespersen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark.
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Niu C, Fan Z, Zheng F, Li Y, Liu C, Wang J, Li Q. Isolation and identification of gas-producing spoilage microbes in fermented broad bean paste. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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32
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Thakur MP, Reich PB, Hobbie SE, Stefanski A, Rich R, Rice KE, Eddy WC, Eisenhauer N. Reduced feeding activity of soil detritivores under warmer and drier conditions. NATURE CLIMATE CHANGE 2018; 8:75-78. [PMID: 29375673 PMCID: PMC5777625 DOI: 10.1038/s41558-017-0032-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Anthropogenic warming is projected to trigger positive feedbacks to climate by enhancing carbon losses from the soil1. While such losses are, in part, owing to increased decomposition of organic matter by invertebrate detritivores, it is unknown how detritivore feeding activity will change with warming2, especially under drought conditions. Here, using four year manipulation experiments in two North American boreal forests, we investigate how temperature (ambient, +1.7 °C, +3.4 °C) and rainfall (ambient, -40% summer precipitation) perturbations influence detritivore feeding activity. In contrast to general expectations1,3, warming had negligible net effects on detritivore feeding activity at ambient precipitation. However, when combined with precipitation reductions, warming decreased feeding activity by ~14%. As across all plots and dates, detritivore feeding activity was positively associated to bulk soil microbial respiration, our results suggest slower rates of decomposition of soil organic matter, and thus reduced positive feedbacks to climate under anthropogenic climate change.
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Affiliation(s)
- Madhav P. Thakur
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Peter B. Reich
- Department of Forest Resources, University of Minnesota, 1530 North Cleveland Avenue, St. Paul, MN 55108, USA
- Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, NSW, 2751, Australia
| | - Sarah E. Hobbie
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Artur Stefanski
- Department of Forest Resources, University of Minnesota, 1530 North Cleveland Avenue, St. Paul, MN 55108, USA
| | - Roy Rich
- Department of Forest Resources, University of Minnesota, 1530 North Cleveland Avenue, St. Paul, MN 55108, USA
| | - Karen E. Rice
- Department of Forest Resources, University of Minnesota, 1530 North Cleveland Avenue, St. Paul, MN 55108, USA
| | - William C. Eddy
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103 Leipzig, Germany
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Blaya J, Barzideh Z, LaPointe G. Symposium review: Interaction of starter cultures and nonstarter lactic acid bacteria in the cheese environment. J Dairy Sci 2017; 101:3611-3629. [PMID: 29274982 DOI: 10.3168/jds.2017-13345] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 10/24/2017] [Indexed: 12/21/2022]
Abstract
The microbiota of ripening cheese is dominated by lactic acid bacteria, which are either added as starters and adjunct cultures or originate from the production and processing environments (nonstarter or NSLAB). After curd formation and pressing, starters reach high numbers, but their viability then decreases due to lactose depletion, salt addition, and low pH and temperature. Starter autolysis releases cellular contents, including nutrients and enzymes, into the cheese matrix. During ripening, NSLAB may attain cell densities up to 8 log cfu per g after 3 to 9 mo. Depending on the species and strain, their metabolic activity may contribute to defects or inconsistency in cheese quality and to the development of typical cheese flavor. The availability of gene and genome sequences has enabled targeted detection of specific cheese microbes and their gene expression over the ripening period. Integrated systems biology is needed to combine the multiple perspectives of post-genomics technologies to elucidate the metabolic interactions among microorganisms. Future research should delve into the variation in cell physiology within the microbial populations, because spatial distribution within the cheese matrix will lead to microenvironments that could affect localized interactions of starters and NSLAB. Microbial community modeling can contribute to improving the efficiency and reduce the cost of food processes such as cheese ripening.
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Affiliation(s)
- J Blaya
- Department of Food Science, University of Guelph, Ontario, Canada N1G 2W1
| | - Z Barzideh
- Department of Food Science, University of Guelph, Ontario, Canada N1G 2W1
| | - G LaPointe
- Department of Food Science, University of Guelph, Ontario, Canada N1G 2W1.
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Bagheri B, Bauer FF, Setati ME. The Impact of Saccharomyces cerevisiae on a Wine Yeast Consortium in Natural and Inoculated Fermentations. Front Microbiol 2017; 8:1988. [PMID: 29085347 PMCID: PMC5650610 DOI: 10.3389/fmicb.2017.01988] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/27/2017] [Indexed: 11/25/2022] Open
Abstract
Natural, also referred to as spontaneous wine fermentations, are carried out by the native microbiota of the grape juice, without inoculation of selected, industrially produced yeast or bacterial strains. Such fermentations are commonly initiated by non-Saccharomyces yeast species that numerically dominate the must. Community composition and numerical dominance of species vary significantly between individual musts, but Saccharomyces cerevisiae will in most cases dominate the late stages of the fermentation and complete the process. Nevertheless, non-Saccharomyces species contribute significantly, positively or negatively, to the character and quality of the final product. The contribution is species and strain dependent and will depend on each species or strain's absolute and relative contribution to total metabolically active biomass, and will therefore, be a function of its relative fitness within the microbial ecosystem. However, the population dynamics of multispecies fermentations are not well understood. Consequently, the oenological potential of the microbiome in any given grape must, can currently not be evaluated or predicted. To better characterize the rules that govern the complex wine microbial ecosystem, a model yeast consortium comprising eight species commonly encountered in South African grape musts and an ARISA based method to monitor their dynamics were developed and validated. The dynamics of these species were evaluated in synthetic must in the presence or absence of S. cerevisiae using direct viable counts and ARISA. The data show that S. cerevisiae specifically suppresses certain species while appearing to favor the persistence of other species. Growth dynamics in Chenin blanc grape must fermentation was monitored only through viable counts. The interactions observed in the synthetic must, were upheld in the natural must fermentations, suggesting the broad applicability of the observed ecosystem dynamics. Importantly, the presence of indigenous yeast populations did not appear to affect the broad interaction patterns between the consortium species. The data show that the wine ecosystem is characterized by both mutually supportive and inhibitory species. The current study presents a first step in the development of a model to predict the oenological potential of any given wine mycobiome.
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Affiliation(s)
| | | | - Mathabatha E. Setati
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch University, Stellenbosch, South Africa
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Silvetti T, Capra E, Morandi S, Cremonesi P, Decimo M, Gavazzi F, Giannico R, De Noni I, Brasca M. Microbial population profile during ripening of Protected Designation of Origin (PDO) Silter cheese, produced with and without autochthonous starter culture. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.06.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Dombrowski N, Seitz KW, Teske AP, Baker BJ. Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments. MICROBIOME 2017; 5:106. [PMID: 28835260 PMCID: PMC5569505 DOI: 10.1186/s40168-017-0322-2] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 08/01/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Deep-sea hydrothermal vents are hotspots for productivity and biodiversity. Thermal pyrolysis and circulation produce fluids rich in hydrocarbons and reduced compounds that stimulate microbial activity in surrounding sediments. Several studies have characterized the diversity of Guaymas Basin (Gulf of California) sediment-inhabiting microorganisms; however, many of the identified taxa lack cultures or genomic representations. Here, we resolved the metabolic potential and community-level interactions of these diverse communities by reconstructing and analyzing microbial genomes from metagenomic sequencing data. RESULTS We reconstructed 115 microbial metagenome-assembled genomes comprising 27 distinct archaeal and bacterial phyla. The archaea included members of the DPANN and TACK superphyla, Bathyarchaeota, novel Methanosarcinales (GoM-Arc1), and anaerobic methane-oxidizing lineages (ANME-1). Among the bacterial phyla, members of the Bacteroidetes, Chloroflexi, and Deltaproteobacteria were metabolically versatile and harbored potential pathways for hydrocarbon and lipid degradation and a variety of respiratory processes. Genes encoding enzymes that activate anaerobic hydrocarbons for degradation were detected in Bacteroidetes, Chloroflexi, Latescibacteria, and KSB1 phyla, while the reconstructed genomes for most candidate bacteria phyla (Aminicenantes, Atribacteria, Omnitrophica, and Stahlbacteria) indicated a fermentative metabolism. Newly obtained GoM-Arc1 archaeal genomes encoded novel pathways for short-chain hydrocarbon oxidation by alkyl-coenzyme M formation. We propose metabolic linkages among different functional groups, such as fermentative community members sharing substrate-level interdependencies with sulfur- and nitrogen-cycling microbes. CONCLUSIONS Overall, inferring the physiologies of archaea and bacteria from metagenome-assembled genomes in hydrothermal deep-sea sediments has revealed potential mechanisms of carbon cycling in deep-sea sediments. Our results further suggest a network of biogeochemical interdependencies in organic matter utilization, hydrocarbon degradation, and respiratory sulfur cycling among deep-sea-inhabiting microbial communities.
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Affiliation(s)
- Nina Dombrowski
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX USA
| | - Kiley W. Seitz
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX USA
| | - Andreas P. Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Brett J. Baker
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX USA
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Chen J, Li Y, Yang Y, Sun H. How cushion communities are maintained in alpine ecosystems: A review and case study on alpine cushion plant reproduction. PLANT DIVERSITY 2017; 39:221-228. [PMID: 30159515 PMCID: PMC6112308 DOI: 10.1016/j.pld.2017.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 07/16/2017] [Accepted: 07/18/2017] [Indexed: 05/07/2023]
Abstract
Cushion species occur in nearly all alpine environments worldwide. In past decades, the adaptive and ecosystem-engineering roles of such highly specialized life forms have been well studied. However, the adaptive strategies responsible for cushion species reproductive success and maintenance in severe alpine habitats remain largely unclear. In this study, we reviewed the current understanding of reproductive strategies and population persistence in alpine cushion species. We then present a preliminary case study on the sexual reproduction of Arenaria polytrichoides (Caryophyllaceae), a typical cushion species inhabiting high elevations of the Himalaya Hengduan Mountains, which is a hotspot for diversification of cushion species. Finally, we highlight the limitations of our current understanding of alpine cushion species reproduction and propose future directions for study.
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Affiliation(s)
- Jianguo Chen
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yanbo Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Corresponding author.
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Corresponding author. Fax: +86 871 65215002.
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Bacterial Physiological Adaptations to Contrasting Edaphic Conditions Identified Using Landscape Scale Metagenomics. mBio 2017; 8:mBio.00799-17. [PMID: 28679747 PMCID: PMC5573673 DOI: 10.1128/mbio.00799-17] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Environmental factors relating to soil pH are important regulators of bacterial taxonomic biodiversity, yet it remains unclear if such drivers affect community functional potential. To address this, we applied whole-genome metagenomics to eight geographically distributed soils at opposing ends of a landscape soil pH gradient (where “low-pH” is ~pH 4.3 and “high-pH” is ~pH 8.3) and evaluated functional differences with respect to functionally annotated genes. First, differences in taxonomic and functional diversity between the two pH categories were assessed with respect to alpha diversity (mean sample richness) and gamma diversity (total richness pooled for each pH category). Low-pH soils, also exhibiting higher organic matter and moisture, consistently had lower taxonomic alpha and gamma diversity, but this was not apparent in assessments of functional alpha and gamma diversity. However, coherent changes in the relative abundances of annotated genes between low- and high-pH soils were identified; with strong multivariate clustering of samples according to pH independent of geography. Assessment of indicator genes revealed that the acidic organic-rich soils possessed a greater abundance of cation efflux pumps, C and N direct fixation systems, and fermentation pathways, indicating adaptations to both acidity and anaerobiosis. Conversely, high-pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings highlight the distinctive physiological adaptations required for bacteria to survive in soils of various nutrient availability and edaphic conditions and more generally indicate that bacterial functional versatility with respect to functional gene annotations may not be constrained by taxonomy. Over a set of soil samples spanning Britain, the widely reported reductions in bacterial taxonomic richness at low pH were found not to be accompanied by significant reductions in the richness of functional genes. However, consistent changes in the abundance of related functional genes were observed, characteristic of differential ecological and nutrient acquisition strategies between high-pH mineral soils and low-pH organic anaerobic soils. Our assessment at opposing ends of a soil gradient encapsulates the limits of functional diversity in temperate climates and identifies key pathways that may serve as indicators for soil element cycling and C storage processes in other soil systems. To this end, we make available a data set identifying functional indicators of the different soils; as well as raw sequences, which given the geographic scale of our sampling should be of value in future studies assessing novel genetic diversity of a wide range of soil functional attributes.
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Walsh AM, Crispie F, Claesson MJ, Cotter PD. Translating Omics to Food Microbiology. Annu Rev Food Sci Technol 2017; 8:113-134. [DOI: 10.1146/annurev-food-030216-025729] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Aaron M. Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Marcus J. Claesson
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
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Shahsavan S, Owlia P, Rastegar Lari A, Bakhshi B, Nobakht M. Investigation of Efflux-Mediated Tetracycline Resistance in Shigella Isolates Using the Inhibitor and Real Time Polymerase Chain Reaction Method. IRANIAN JOURNAL OF PATHOLOGY 2017; 12:53-61. [PMID: 29760753 PMCID: PMC5938724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 01/27/2017] [Indexed: 11/05/2022]
Abstract
BACKGROUND Shigella spp. are gram negative bacteria, which are of global public health importance. The growing of multidrug-resistant Shigella isolates are a major problem around the world. METHODS Overall, 50 isolates of Shigella spp. from children diarrheic stools were studied. The isolates were identified and confirmed using biochemical, serological and molecular methods (ipaH, wbgZ and rfc genes). Antimicrobial susceptibility test was done according to the Clinical and Laboratory Standards Institute (CLSI) guidelines against minocycline, tetracycline, doxycycline, ampicillin, streptomycin, trimethoprim-sulfamethoxazole, nalidixic acid, norfloxacin, ciprofloxacin and levofloxacin. Also, the role of efflux pump in defense of Shigella against tetracycline was investigated by Minimum Inhibitory Concentration (MIC) with and without an efflux pump inhibitor. Detection of tetA, tetB, tetC and tetD genes in Shigella was evaluated by conventional Polymerase Chain Reaction (PCR) and real time PCR. RESULTS Molecular identification revealed a prevalence of 14% for Shigella flexneri and 86% for Shigella sonnei. Minimum Inhibitory Concentration (MIC) of 90% of resistant isolates was changed in the presence CCCP. Results of conventional PCR exhibited that 66% of isolates were positive for tetA, while according to real time PCR method, 90% of isolates carried tetA. Positive results for tetB were 12% and 18% by conventional and real time PCR methods, respectively. No positive results were detected for tetC and tetD. Also, tetB was detected only in S. flexneri while tetA was detected in both S. flexneri and S. sonnei. CONCLUSION It seems that efflux-mediated tetracycline resistance to tetracycline in S. flexneri can be related to tetB, however resistance in S. sonnei can be related to the expression of tetA.
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Affiliation(s)
- Shadi Shahsavan
- Antimicrobial Resistance research center, Iran University of Medical science, Tehran, Iran
| | - Parviz Owlia
- Molecular Microbiology Research Center, Shahed University, Tehran, IR Iran
| | - Abdolaziz Rastegar Lari
- Dept. of Microbiology, Faculty of Medicine, Iran University of Medical science, Tehran, Iran
| | - Bita Bakhshi
- Dept. of Microbiology, Faculty of Medicine, Tarbiat Modares University, Tehran, Iran
| | - Maliheh Nobakht
- Antimicrobial Resistance research center, Iran University of Medical science, Tehran, Iran,Dept. of Anatomy, Faculty of Medicine, Iran University of Medical science, Tehran, Iran,Corresponding Information: Dr. Maliheh Nobakht, Antimicrobial Resistance research center, Iran University of Medical science, Tehran, Iran. Tel: +982186704566
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Affiliation(s)
- Linda V Thomas
- Yakult UK Limited; Odyssey Business Park West End Road South Ruislip London HA4 6QQ UK
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Osińska A, Harnisz M, Korzeniewska E. Prevalence of plasmid-mediated multidrug resistance determinants in fluoroquinolone-resistant bacteria isolated from sewage and surface water. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:10818-10831. [PMID: 26893181 PMCID: PMC4884563 DOI: 10.1007/s11356-016-6221-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 01/31/2016] [Indexed: 05/04/2023]
Abstract
Fluoroquinolones (FQs) are fully synthetic broad-spectrum antibacterial agents that are becoming increasingly popular in the treatment of clinical and veterinary infections. Being excreted during treatment, mostly as active compounds, their biological action is not limited to the therapeutic site, but it is moved further as resistance selection pressure into the environment. Water environment is an ideal medium for the aggregation and dissemination of antibiotics, antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARGs), which can pose a serious threat to human health. Because of this, the aim of this study was to determine the number of fluoroquinolone-resistant bacteria (FQRB) and their share in total heterotrophic plate counts (HPC) in treated wastewater (TWW), and upstream and downstream river water (URW, DRW) samples where TWW is discharged. The spread of plasmid-mediated quinolone resistance (PMQR) determinants and the presence/absence of resistance genes to other most popular antibiotic groups (against tetracyclines and beta-lactams) in selected 116 multiresistant isolates were investigated. The share of FQRB in total HPC in all samples was rather small and ranged from 0.7 % in URW samples to 7.5 % in TWW. Bacteria from Escherichia (25.0 %), Acinetobacter (25.0 %), and Aeromonas (6.9 %) genera were predominant in the FQRB group. Fluoroquinolone resistance was mostly caused by the presence of the gene aac(6')-1b-cr (91.4 %). More rarely reported was the occurrence of qnrS, qnrD, as well as oqxA, but qnrA, qnrB, qepA, and oqxB were extremely rarely or never noted in FQRB. The most prevalent bacterial genes connected with beta-lactams' resistance in FQRB were bla TEM, bla OXA, and bla CTX-M. The bla SHV was less common in the community of FQRB. The occurrence of bla genes was reported in almost 29.3 % of FQRB. The most abundant tet genes in FQRB were tet(A), tet(L), tet(K), and tet(S). The prevalence of tet genes was observed in 41.4 % of FQRB. The highest prevalence of multidrug-resistant (MDR) microorganisms was detected in TWW and DRW samples. It indicates that discharged TWW harbors multiresistant bacterial strains and that mobile PMQR and ARGs elements may have a selective pressure for species affiliated to bacteria in the river water.
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Affiliation(s)
- Adriana Osińska
- Department of Environmental Microbiology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720, Olsztyn, Poland
| | - Monika Harnisz
- Department of Environmental Microbiology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720, Olsztyn, Poland
| | - Ewa Korzeniewska
- Department of Environmental Microbiology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720, Olsztyn, Poland.
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Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate. Sci Rep 2016; 6:21871. [PMID: 26911915 PMCID: PMC4766472 DOI: 10.1038/srep21871] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/02/2016] [Indexed: 11/29/2022] Open
Abstract
Traditional cheeses harbour complex microbial consortia that play an important role in shaping typical sensorial properties. However, the microbial metabolism is considered difficult to control. Microbial community succession and the related gene expression were analysed during ripening of a traditional Italian cheese, identifying parameters that could be modified to accelerate ripening. Afterwards, we modulated ripening conditions and observed consistent changes in microbial community structure and function. We provide concrete evidence of the essential contribution of non-starter lactic acid bacteria in ripening-related activities. An increase in the ripening temperature promoted the expression of genes related to proteolysis, lipolysis and amino acid/lipid catabolism and significantly increases the cheese maturation rate. Moreover, temperature-promoted microbial metabolisms were consistent with the metabolomic profiles of proteins and volatile organic compounds in the cheese. The results clearly indicate how processing-driven microbiome responses can be modulated in order to optimize production efficiency and product quality.
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Gopal N, Hill C, Ross PR, Beresford TP, Fenelon MA, Cotter PD. The Prevalence and Control of Bacillus and Related Spore-Forming Bacteria in the Dairy Industry. Front Microbiol 2015; 6:1418. [PMID: 26733963 PMCID: PMC4685140 DOI: 10.3389/fmicb.2015.01418] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/30/2015] [Indexed: 01/14/2023] Open
Abstract
Milk produced in udder cells is sterile but due to its high nutrient content, it can be a good growth substrate for contaminating bacteria. The quality of milk is monitored via somatic cell counts and total bacterial counts, with prescribed regulatory limits to ensure quality and safety. Bacterial contaminants can cause disease, or spoilage of milk and its secondary products. Aerobic spore-forming bacteria, such as those from the genera Sporosarcina, Paenisporosarcina, Brevibacillus, Paenibacillus, Geobacillus and Bacillus, are a particular concern in this regard as they are able to survive industrial pasteurization and form biofilms within pipes and stainless steel equipment. These single or multiple-species biofilms become a reservoir of spoilage microorganisms and a cycle of contamination can be initiated. Indeed, previous studies have highlighted that these microorganisms are highly prevalent in dead ends, corners, cracks, crevices, gaskets, valves and the joints of stainless steel equipment used in the dairy manufacturing plants. Hence, adequate monitoring and control measures are essential to prevent spoilage and ensure consumer safety. Common controlling approaches include specific cleaning-in-place processes, chemical and biological biocides and other novel methods. In this review, we highlight the problems caused by these microorganisms, and discuss issues relating to their prevalence, monitoring thereof and control with respect to the dairy industry.
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Affiliation(s)
- Nidhi Gopal
- Teagasc Food Research CentreCork, Ireland
- School of Microbiology, University College CorkCork, Ireland
| | - Colin Hill
- School of Microbiology, University College CorkCork, Ireland
- APC Microbiome InstituteCork, Ireland
| | - Paul R. Ross
- College of Science, Engineering and Food Science, University College CorkCork, Ireland
| | | | | | - Paul D. Cotter
- Teagasc Food Research CentreCork, Ireland
- APC Microbiome InstituteCork, Ireland
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O'Sullivan DJ, Fallico V, O'Sullivan O, McSweeney PLH, Sheehan JJ, Cotter PD, Giblin L. High-throughput DNA sequencing to survey bacterial histidine and tyrosine decarboxylases in raw milk cheeses. BMC Microbiol 2015; 15:266. [PMID: 26577209 PMCID: PMC4650399 DOI: 10.1186/s12866-015-0596-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 11/02/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The aim of this study was to employ high-throughput DNA sequencing to assess the incidence of bacteria with biogenic amine (BA; histamine and tyramine) producing potential from among 10 different cheeses varieties. To facilitate this, a diagnostic approach using degenerate PCR primer pairs that were previously designed to amplify segments of the histidine (hdc) and tyrosine (tdc) decarboxylase gene clusters were employed. In contrast to previous studies in which the decarboxylase genes of specific isolates were studied, in this instance amplifications were performed using total metagenomic DNA extracts. RESULTS Amplicons were initially cloned to facilitate Sanger sequencing of individual gene fragments to ensure that a variety of hdc and tdc genes were present. Once this was established, high throughput DNA sequencing of these amplicons was performed to provide a more in-depth analysis of the histamine- and tyramine-producing bacteria present in the cheeses. High-throughput sequencing resulted in generation of a total of 1,563,764 sequencing reads and revealed that Lactobacillus curvatus, Enterococcus faecium and E. faecalis were the dominant species with tyramine producing potential, while Lb. buchneri was found to be the dominant species harbouring histaminogenic potential. Commonly used cheese starter bacteria, including Streptococcus thermophilus and Lb. delbreueckii, were also identified as having biogenic amine producing potential in the cheese studied. Molecular analysis of bacterial communities was then further complemented with HPLC quantification of histamine and tyramine in the sampled cheeses. CONCLUSIONS In this study, high-throughput DNA sequencing successfully identified populations capable of amine production in a variety of cheeses. This approach also gave an insight into the broader hdc and tdc complement within the various cheeses. This approach can be used to detect amine producing communities not only in food matrices but also in the production environment itself.
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Affiliation(s)
- Daniel J O'Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland.
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland.
| | | | - Orla O'Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland.
| | - Paul L H McSweeney
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland.
| | | | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland.
- Alimentary Pharmabiotic Centre, Cork, Ireland.
| | - Linda Giblin
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland.
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Kergourlay G, Taminiau B, Daube G, Champomier Vergès MC. Metagenomic insights into the dynamics of microbial communities in food. Int J Food Microbiol 2015; 213:31-9. [DOI: 10.1016/j.ijfoodmicro.2015.09.010] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 09/04/2015] [Accepted: 09/13/2015] [Indexed: 02/06/2023]
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48
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Hickey CD, Sheehan JJ, Wilkinson MG, Auty MAE. Growth and location of bacterial colonies within dairy foods using microscopy techniques: a review. Front Microbiol 2015; 6:99. [PMID: 25741328 PMCID: PMC4332360 DOI: 10.3389/fmicb.2015.00099] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/26/2015] [Indexed: 11/13/2022] Open
Abstract
The growth, location, and distribution of bacterial colonies in dairy products are important factors for the ripening and flavor development of cheeses, yogurts, and soured creams. Starter, non-starter, spoilage, and pathogenic bacteria all become entrapped in the developing casein matrix of dairy foods. In order to visualize these bacterial colonies and the environments surrounding them, microscopy techniques are used. The use of various microscopy methods allow for the rapid detection, enumeration, and distribution of starter, non-starter and pathogenic bacteria in dairy foods. Confocal laser scanning microscopy is extensively utilized to identify bacteria location via the use of fluorescent dyes. Further study is needed in relation to the development of micro- gradients and localized ripening parameters in dairy products due to the location of bacteria at the protein-fat interface. Development in the area of bacterial discrimination using microscopy techniques and fluorescent dyes/tags is needed as the benefits of rapidly identifying spoilage/pathogenic bacteria early in product manufacture would be of huge benefit in relation to both safety and financial concerns.
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Affiliation(s)
- Cian D. Hickey
- Teagasc Food Research CentreFermoy, Ireland
- University of LimerickLimerick, Ireland
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Temporal and spatial differences in microbial composition during the manufacture of a continental-type cheese. Appl Environ Microbiol 2015; 81:2525-33. [PMID: 25636841 DOI: 10.1128/aem.04054-14] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine-salted continental-type cheese in cheeses produced early and late in the production day. Differences in the microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that cheeses produced late in the day had a more diverse microbial population than their early equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were initially found to have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the genera Thermus, Pseudoalteromonas, and Bifidobacterium, not routinely associated with a continental-type cheese produced from pasteurized milk, were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high-throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition.
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Ghasimi DSM, Tao Y, de Kreuk M, Zandvoort MH, van Lier JB. Microbial population dynamics during long-term sludge adaptation of thermophilic and mesophilic sequencing batch digesters treating sewage fine sieved fraction at varying organic loading rates. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:171. [PMID: 26500697 PMCID: PMC4618146 DOI: 10.1186/s13068-015-0355-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/09/2015] [Indexed: 05/16/2023]
Abstract
BACKGROUND In this research, the feasibility of, and population dynamics in, one-step anaerobic sequencing batch reactor systems treating the fine sieved fraction (FSF) from raw municipal wastewater was studied under thermophilic (55 °C) and mesophilic (35 °C) conditions. FSF was sequestered from raw municipal wastewater, in the Netherlands, using a rotating belt filter (mesh size 350 micron). FSF is a heterogeneous substrate that mainly consists of fibres originating from toilet paper and thus contains a high cellulosic fraction (60-80 % of total solids content), regarded as an energy-rich material. RESULTS Results of the 656-day fed-batch operation clearly showed that thermophilic digestion was more stable, applying high organic loading rates (OLR) up to 22 kg COD/(m(3) day). In contrast, the mesophilic digester already failed applying an OLR of 5.5 kg COD/(m(3) day), indicated by a drop in pH and increase in volatile fatty acids (VFAs). The observed viscosity values of the mesophilic sludge were more than tenfold higher than the thermophilic sludge. 454-pyrosequencing of eight mesophilic and eight thermophilic biomass samples revealed that Bacteroides and aceticlastic methanogen Methanosaeta were the dominant genera in the mesophilic digester, whereas OP9 lineages, Clostridium and the hydrogenotrophic methanogen Methanothermobacter dominated the thermophilic one. CONCLUSIONS Our study suggests that applying thermophilic conditions for FSF digestion would result in a higher biogas production rate and/or a smaller required reactor volume, comparing to mesophilic conditions.
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Affiliation(s)
- Dara S. M. Ghasimi
- />Sanitary Engineering Section, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
| | - Yu Tao
- />Sanitary Engineering Section, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
- />Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, SW7 2AZ the UK
| | - Merle de Kreuk
- />Sanitary Engineering Section, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
| | - Marcel H. Zandvoort
- />Waternet, Korte Ouderkerkerdijk 7, P.O. Box 94370, 1090 GJ Amsterdam, The Netherlands
| | - Jules B. van Lier
- />Sanitary Engineering Section, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
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