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Giordano I, Pasolli E, Mauriello G. Transcriptomic analysis reveals differential gene expression patterns of Lacticaseibacillus casei ATCC 393 in response to ultrasound stress. ULTRASONICS SONOCHEMISTRY 2024; 107:106939. [PMID: 38843696 PMCID: PMC11214525 DOI: 10.1016/j.ultsonch.2024.106939] [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: 04/08/2024] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/19/2024]
Abstract
In recent years, there has been a growing interest in modulating the performance of probiotic, mainly Lactic Acid Bacteria (LAB), in the field of probiotic food. Attenuation, induced by sub-lethal stresses, delays the probiotic metabolism, and induces a metabolic shift as survival strategy. In this paper, RNA sequencing was used to uncover the transcriptional regulation in Lacticaseibacillus casei ATCC 393 after ultrasound-induced attenuation. Six (T) and 8 (ST) min of sonication induced a significant differential expression of 742 and 409 genes, respectively. We identified 198 up-regulated and 321 down-regulated genes in T, and similarly 321 up-regulated and 249 down-regulated in ST. These results revealed a strong defensive response at 6 min, followed by adaptation at 8 min. Ultrasound attenuation modified the expression of genes related to a series of crucial biomolecular processes including membrane transport, carbohydrate and purine metabolism, phage-related genes, and translation. Specifically, genes encoding PTS transporters and genes involved in the glycolytic pathway and pyruvate metabolism were up-regulated, indicating an increased need for energy supply, as also suggested by an increase in the transcription of purine biosynthetic genes. Instead, protein translation, a high-energy process, was inhibited with the down-regulation of ribosomal protein biosynthetic genes. Moreover, phage-related genes were down-regulated suggesting a tight transcriptional control on DNA structure. The observed phenomena highlight the cell need of ATP to cope with the multiple ultrasound stresses and the activation of processes to stabilize and preserve the DNA structure. Our work demonstrates that ultrasound has remarkable effects on the tested strain and elucidates the involvement of different pathways in its defensive stress-response and in the modification of its phenotype.
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Affiliation(s)
- Irene Giordano
- Department of Agricultural Sciences, University of Naples Federico II, 80049 Naples, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, 80049 Naples, Italy
| | - Gianluigi Mauriello
- Department of Agricultural Sciences, University of Naples Federico II, 80049 Naples, Italy.
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2
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Araoz M, Grillo-Puertas M, de Moreno de LeBlanc A, Hebert EM, Villegas JM, Rapisarda VA. Inorganic phosphate modifies stationary phase fitness and metabolic pathways in Lactiplantibacillus paraplantarum CRL 1905. Front Microbiol 2024; 15:1343541. [PMID: 38476941 PMCID: PMC10927959 DOI: 10.3389/fmicb.2024.1343541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/19/2024] [Indexed: 03/14/2024] Open
Abstract
Inorganic phosphate (Pi) concentration modulates polyphosphate (polyP) levels in diverse bacteria, affecting their physiology and survival. Lactiplantibacillus paraplantarum CRL 1905 is a lactic acid bacterium isolated from quinoa sourdough with biotechnological potential as starter, for initiating fermentation processes in food, and as antimicrobial-producing organism. The aim of this work was to evaluate the influence of the environmental Pi concentration on different physiological and molecular aspects of the CRL 1905 strain. Cells grown in a chemically defined medium containing high Pi (CDM + P) maintained elevated polyP levels up to late stationary phase and showed an enhanced bacterial survival and tolerance to oxidative stress. In Pi sufficiency condition (CDM-P), cells were ~ 25% longer than those grown in CDM + P, presented membrane vesicles and a ~ 3-fold higher capacity to form biofilm. Proteomic analysis indicated that proteins involved in the "carbohydrate transport and metabolism" and "energy production and conversion" categories were up-regulated in high Pi stationary phase cells, implying an active metabolism in this condition. On the other hand, stress-related chaperones and enzymes involved in cell surface modification were up-regulated in the CDM-P medium. Our results provide new insights to understand the CRL 1905 adaptations in response to differential Pi conditions. The adjustment of environmental Pi concentration constitutes a simple strategy to improve the cellular fitness of L. paraplantarum CRL 1905, which would benefit its potential as a microbial cell factory.
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Affiliation(s)
- Mario Araoz
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica, “Dr. Bernabé Bloj”, Facultad de Bioquímica, Química y Farmacia, UNT, San Miguel de Tucumán, Argentina
| | - Mariana Grillo-Puertas
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica, “Dr. Bernabé Bloj”, Facultad de Bioquímica, Química y Farmacia, UNT, San Miguel de Tucumán, Argentina
| | | | - Elvira María Hebert
- Centro de Referencia para Lactobacilos (CERELA-CONICET), San Miguel de Tucumán, Argentina
| | - Josefina María Villegas
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica, “Dr. Bernabé Bloj”, Facultad de Bioquímica, Química y Farmacia, UNT, San Miguel de Tucumán, Argentina
| | - Viviana Andrea Rapisarda
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica, “Dr. Bernabé Bloj”, Facultad de Bioquímica, Química y Farmacia, UNT, San Miguel de Tucumán, Argentina
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3
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Zhang Q, Zúñiga M, Alcántara C, Wolf D, Mascher T, Revilla-Guarinos A. Cross-regulation of Aps-promoters in Lacticaseibacillus paracasei by the PsdR response regulator in response to lantibiotics. Sci Rep 2024; 14:3319. [PMID: 38336830 PMCID: PMC10858260 DOI: 10.1038/s41598-024-53592-1] [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: 08/10/2023] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
The PsdRSAB and ApsRSAB detoxification modules, together with the antimicrobial peptides (AMPs)-resistance determinants Dlt system and MprF protein, play major roles in the response to AMPs in Lacticaseibacillus paracasei BL23. Sensitivity assays with a collection of mutants showed that the PsdAB ABC transporter and the Dlt system are the main subtilin resistance determinants. Quantification of the transcriptional response to subtilin indicate that this response is exclusively regulated by the two paralogous systems PsdRSAB and ApsRSAB. Remarkably, a cross-regulation of the derAB, mprF and dlt-operon genes-usually under control of ApsR-by PsdR in response to subtilin was unveiled. The high similarity of the predicted structures of both response regulators (RR), and of the RR-binding sites support this possibility, which we experimentally verified by protein-DNA binding studies. ApsR-P shows a preferential binding in the order PderA > Pdlt > PmprF > PpsdA. However, PsdR-P bound with similar apparent affinity constants to the four promoters. This supports the cross-regulation of derAB, mprF and the dlt-operon by PsdR. The possibility of cross-regulation at the level of RR-promoter interaction allows some regulatory overlap with two RRs controlling the expression of systems involved in maintenance of critical cell membrane functions in response to lantibiotics.
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Affiliation(s)
- Qian Zhang
- Chair of General Microbiology, Technische Universität Dresden, 01217, Dresden, Germany
| | - Manuel Zúñiga
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), 46980, Paterna, Valencia, Spain
| | - Cristina Alcántara
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), 46980, Paterna, Valencia, Spain
| | - Diana Wolf
- Chair of General Microbiology, Technische Universität Dresden, 01217, Dresden, Germany
| | - Thorsten Mascher
- Chair of General Microbiology, Technische Universität Dresden, 01217, Dresden, Germany.
| | - Ainhoa Revilla-Guarinos
- Chair of General Microbiology, Technische Universität Dresden, 01217, Dresden, Germany.
- Oral Microbiome Group, Genomics and Health Department, FISABIO Foundation, 46020, Valencia, Spain.
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4
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Li T, Wang X, Li C, Fu Q, Shi X, Wang B. Investigation of Acid Tolerance Mechanism of Acetobacter pasteurianus under Different Concentrations of Substrate Acetic Acid Based on 4D Label-Free Proteomic Analysis. Foods 2023; 12:4471. [PMID: 38137274 PMCID: PMC10742644 DOI: 10.3390/foods12244471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Acetobacter pasteurianus is always used to brew vinegar because of its ability of producing and tolerating a high concentration of acetic acid. During vinegar fermentation, initial acetic acid contributes to acetic acid accumulation, which varies with initial concentrations. In this study, to investigate the mechanisms of tolerating and producing acetic acid of Acetobacter pasteurianus under different concentrations of substrate acetic acid, four-dimensional label-free proteomic technology has been used to analyze the protein profiles of Acetobacter pasteurianus at different growth stages (the lag and exponential phases) and different substrate acetic acid concentrations (0%, 3%, and 6%). A total of 2093 proteins were quantified in this study. The differentially expressed proteins were majorly involved in gene ontology terms of metabolic processes, cellular metabolic processes, and substance binding. Under acetic acid stress, strains might attenuate the toxicity of acetic acid by intensifying fatty acid metabolism, weakening the tricarboxylic acid cycle, glycerophospholipid and energy metabolism during the lag phase, while strains might promote the assimilation of acetic acid and inter-conversion of substances during the exponential phase by enhancing the tricarboxylic acid cycle, glycolysis, pyruvate, and energy metabolism to produce and tolerate acid. Besides, cell cycle regulation and protein translation might be potential acid tolerance pathways under high acid stress. The result contributes to the exploration of new potential acid tolerance mechanisms in Acetobacter pasteurianus from four-dimensional label-free relative quantitative proteomics analysis.
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Affiliation(s)
| | | | | | | | | | - Bin Wang
- Food College, Shihezi University, Shihezi 832000, China
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5
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Gao L, Shi W, Xia X. Genomic Plasticity of Acid-Tolerant Phenotypic Evolution in Acetobacter pasteurianus. Appl Biochem Biotechnol 2023; 195:6003-6019. [PMID: 36738389 DOI: 10.1007/s12010-023-04353-9] [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] [Accepted: 01/10/2023] [Indexed: 02/05/2023]
Abstract
Acetic acid bacteria have a remarkable capacity to cope with elevated concentrations of cytotoxic acetic acid in their fermentation environment. In particular, the high-level acetate tolerance of Acetobacter pasteurianus that occurs in vinegar industrial settings must be constantly selected for. However, the improved acetic acid tolerance is rapidly lost without a selection pressure. To understand genetic and molecular biology of this acquired acetic acid tolerance in A. pasteurianus, we evolved three strains A. pasteurianus CICIM B7003, CICIM B7003-02, and ATCC 33,445 over 960 generations (4 months) in two initial acetic acids of 20 g·L-1 and 30 g·L-1, respectively. An acetic acid-adapted strain M20 with significantly improved specific growth rate of 0.159 h-1 and acid productivity of 1.61 g·L-1·h-1 was obtained. Comparative genome analysis of six evolved strains revealed that the genetic variations of adaptation were mainly focused on lactate metabolism, membrane proteins, transcriptional regulators, transposases, replication, and repair system. Among of these, lactate dehydrogenase, acetolactate synthase, glycosyltransferase, ABC transporter ATP-binding protein, two-component regulatory systems, the type II toxin-antitoxin system (RelE/RelB/StbE), exodeoxyribonuclease III, type I restriction endonuclease, tRNA-uridine 2-sulfurtransferase, and transposase might collaboratively contribute to the improved acetic acid tolerance in A. pasteurianus strains. The balance between repair factors and transposition variations might be the basis for genomic plasticity of A. pasteurianus strains, allowing the survival of populations and their offspring in acetic acid stress fluctuations. These observations provide important insights into the nature of acquired acetic acid tolerance phenotype and lay a foundation for future genetic manipulation of these strains.
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Affiliation(s)
- Ling Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Wei Shi
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.
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6
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Yang Y, Song X, Xiong Z, Xia Y, Wang G, Ai L. Complete Genome Sequence of Lactobacillus salivarius AR809, a Probiotic Strain with Oropharyngeal Tract Resistance and Adhesion to the Oral Epithelial Cells. Curr Microbiol 2022; 79:280. [PMID: 35934757 DOI: 10.1007/s00284-022-02963-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 07/06/2022] [Indexed: 11/26/2022]
Abstract
Lactobacillus salivarius AR809 was isolated from a healthy adult oral cavity with multiple probiotic properties, such as high antimicrobial activity, adhesion to the oral epithelium, resistance to acidic pH, bile, lysozyme, and H2O2. In this study, to investigate the genetic basis on probiotic potential and identify the functional genes in the strain, the complete genome of strain AR809 was sequenced by Illumina and PacBio platforms. Then comparative genome analysis on 11 strains of Lactobacillus salivarius was performed. The complete genome of AR809 consisted of a circular 1,747,224 bp chromosome with 33.00% GC content and four circular plasmids [pA (247,948 bp), pB (27,292 bp), pC (3349 bp), and pD (2898 bp), respectively]. From among the 1866 protein-coding genes, 130 carbohydrate metabolism-related genes, 18 bacteriocin biosynthesis-related genes, 74 environmental stress-related genes, and a series of adhesion-related genes were identified via clusters of orthologous genes, Koyto Encyclopedia of Genes and Genomes, and carbohydrate-active enzymes annotation. The comparative genome analysis indicated that genomic homology between AR809 and CICC23174 was the highest. In conclusion, the present work provided valuable insights into the gene's function prediction and understanding the genetic basis on adapting to host oropharyngeal-gastrointestinal tract in strain AR809.
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Affiliation(s)
- Yong Yang
- University of Shanghai for Science and Technology, Shanghai Engineering Research Center of Food Microbiology, Shanghai, 200093, China
| | - Xin Song
- University of Shanghai for Science and Technology, Shanghai Engineering Research Center of Food Microbiology, Shanghai, 200093, China
| | - Zhiqiang Xiong
- University of Shanghai for Science and Technology, Shanghai Engineering Research Center of Food Microbiology, Shanghai, 200093, China
| | - Yongjun Xia
- University of Shanghai for Science and Technology, Shanghai Engineering Research Center of Food Microbiology, Shanghai, 200093, China
| | - Guangqiang Wang
- University of Shanghai for Science and Technology, Shanghai Engineering Research Center of Food Microbiology, Shanghai, 200093, China
| | - Lianzhong Ai
- University of Shanghai for Science and Technology, Shanghai Engineering Research Center of Food Microbiology, Shanghai, 200093, China.
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7
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Padilla P, Estévez M, Andrade MJ, Peña FJ, Delgado J. Proteomics reveal the protective effects of chlorogenic acid on Enterococcus faecium Q233 in a simulated pro-oxidant colonic environment. Food Res Int 2022; 157:111464. [PMID: 35761697 DOI: 10.1016/j.foodres.2022.111464] [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: 03/28/2022] [Revised: 05/29/2022] [Accepted: 06/01/2022] [Indexed: 11/26/2022]
Abstract
Certain phytochemicals have been found to promote the beneficial effects of probiotic bacteria although the molecular mechanisms of such interactions are poorly understood. The objective of the present study was to evaluate the impact of the exposure to 0.5 mM chlorogenic acid (CA) on the redox status and proteome of Enterococcus faecium isolated from cheese and challenged with 2.5 mM hydrogen peroxide (H2O2). The bacterium was incubated in anaerobic conditions for 48 h at 37 °C. CA exposure led to a more intense oxidative stress and accretion of bacterial protein carbonyls than those induced by H2O2. The oxidative damage to bacterial proteins was even more severe in the bacterium treated with both CA and H2O2, yet, such combination led to a strengthening of the antioxidant defenses, namely, a catalase-like activity. The proteomic study indicated that H2O2 caused a decrease in energy supply and the bacterium responded by reinforcing the membrane and wall structures and counteracting the redox and pH imbalance. CA stimulated the accretion of proteins related to translation and transcription regulators, and hydrolases. This phytochemical was able to counteract certain proteomic changes induced by H2O2 (i.e. increase of ATP binding cassete (ABC) transporter complex) and cause the increase of Rex, a redox-sensitive protein implicated in controlling metabolism and responses to oxidative stress. Although this protection should be confirmed under in vivo conditions, such effects point to benefits in animals or humans affected by disorders in which oxidative stress plays a major role.
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Affiliation(s)
- P Padilla
- Food Technology and Quality (TECAL), Institute of Meat and Meat Products (IPROCAR), University of Extremadura, Cáceres, Spain; Food Hygiene and Safety (HISEALI), Institute of Meat and Meat Products (IPROCAR), University of Extremadura, Cáceres, Spain
| | - M Estévez
- Food Technology and Quality (TECAL), Institute of Meat and Meat Products (IPROCAR), University of Extremadura, Cáceres, Spain.
| | - M J Andrade
- Food Hygiene and Safety (HISEALI), Institute of Meat and Meat Products (IPROCAR), University of Extremadura, Cáceres, Spain
| | - F J Peña
- Spermatology Laboratory, University of Extremadura, Cáceres, Spain
| | - J Delgado
- Food Hygiene and Safety (HISEALI), Institute of Meat and Meat Products (IPROCAR), University of Extremadura, Cáceres, Spain
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Wen ZT, Huang X, Ellepola K, Liao S, Li Y. Lactobacilli and human dental caries: more than mechanical retention. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35671222 DOI: 10.1099/mic.0.001196] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lactobacilli have been considered as major contributors to human dental caries for over a century. Recent in vitro model studies have shown that when compared to Streptococcus mutans, a keystone pathogen of human dental caries, the ability of lactobacilli to form biofilms is poor, although differences exist between the different major species. Further studies using molecular and bioinformatics approaches provide evidence that multiple mechanisms, including adhesin-receptor mediated physical contact with S. mutans, facilitate the adherence and establishment of lactobacilli on the tooth surface. There is also evidence that under conditions like continuous sugar consumption, weak acids and other antimicrobials such as bacteriocins from lactobacilli can become detrimental to the microbial community, especially those in the proximity. Details on the underlying mechanisms of how different Lactobacillus sp. establish and persist in the highly complex microbiota on the tooth surface await further investigation.
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Affiliation(s)
- Zezhang T Wen
- Department of Prosthodontics, School of Dentistry and Department of Microbiology, Immunology and Parasitology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Xiaochang Huang
- Department of Prosthodontics, School of Dentistry and Department of Microbiology, Immunology and Parasitology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA.,Present address: Analysis and Testing Center, Nanchang University, 235 Nanjing East Load, Qingshan Lake District, Nanchang, PR China
| | - Kassapa Ellepola
- Department of Prosthodontics, School of Dentistry and Department of Microbiology, Immunology and Parasitology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA.,Present address: Department of Oral Biology, College of Dentistry, University of Illinois Chicago, Chicago, IL, USA
| | - Sumei Liao
- Department of Prosthodontics, School of Dentistry and Department of Microbiology, Immunology and Parasitology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Yihong Li
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornel University, Ithaca, NY, USA
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Okoye CO, Dong K, Wang Y, Gao L, Li X, Wu Y, Jiang J. Comparative genomics reveals the organic acid biosynthesis metabolic pathways among five lactic acid bacterial species isolated from fermented vegetables. N Biotechnol 2022; 70:73-83. [PMID: 35525431 DOI: 10.1016/j.nbt.2022.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/28/2022] [Accepted: 05/02/2022] [Indexed: 10/18/2022]
Abstract
Lactic acid bacteria (LAB) comprise a widespread bacterial group, inhabiting the niches of fermented vegetables and capable of producing beneficial organic acids. In the present study, several bioinformatics approaches were used to perform whole-genome sequencing and comparative genomics of five LAB species, Lactobacillus plantarum PC1-1, Pediococcus pentosaceus PC2-1(F2), Weissella hellenica PC1A, Lactobacillus buchneri PC-C1, and Enterococcus sp. YC2-6, to enhance understanding of their different genetic functionalities and organic acid biosynthesis. The results revealed major carbohydrate-active enzymes, putative operons and unique mobile genetic elements, including plasmids, resistance genes, insertion sequences and composite transposons involved in organic acid biosynthesis. The metabolic pathways of organic acid biosynthesis emphasize the key genes encoding specific enzymes required for organic acid metabolism. The five genomes were found to contain various regions of secondary metabolite biosynthetic gene clusters, including the type III polyketide synthases (T3PKS) enriched with unique genes encoding a hydroxymethylglutaryl-CoA synthase, capable of exhibiting specific antimicrobial activity with biopreservative potential, and a cyclic AMP receptor protein (CPR) transcription factor acting as a glucose sensor in organic acid biosynthesis. This could enable the organisms to prevail in the fermentation process, suggesting potential industrial applications.
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Affiliation(s)
- Charles Obinwanne Okoye
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Department of Zoology & Environmental Biology, University of Nigeria, Nsukka 410001, Nigeria
| | - Ke Dong
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yongli Wang
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Lu Gao
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xia Li
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yanfang Wu
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jianxiong Jiang
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
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10
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Li X, Wang P, Chu S, Xu Y, Su Y, Wu D, Xie B. Short-term biodrying achieves compost maturity and significantly reduces antibiotic resistance genes during semi-continuous food waste composting inoculated with mature compost. JOURNAL OF HAZARDOUS MATERIALS 2022; 427:127915. [PMID: 34863571 DOI: 10.1016/j.jhazmat.2021.127915] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 06/13/2023]
Abstract
Food waste (FW) is important object of resource utilization and source of antibiotic resistance genes (ARGs). This study investigated the effects of biodrying combined with inoculating mature compost (B&M) on the composting efficiency, succession of bacterial communities and their links with metabolism functions as well as the fate of ARGs during FW composting. The results showed that B&M could rapidly raise and maintain high relative abundance of Bacillaceae (66.59-94.44%) as well as composting temperature (45.86-65.86 ℃), so as to achieve the final maturity of FW composting in a short time by regulating microbial carbohydrate (14.02-15.31%) and amino acid metabolism (10.33-12.47%). Network analysis demonstrated that high temperature could effectively inhibit the proliferation and spread of potential bacterial hosts of ARGs and integrons including Lactobacillaceae, Enterobacteriaceae, Leuconostocaceae and Corynebacteriaceae during the first two days of composting. As a result, B&M significantly reduced the absolute (72.09-99.47%) and relative abundances (0.31-2.44 logs) of nearly all ARGs especially ermB, tetM, blaCTX-M and blaOXA. Present study deepened the knowledge of ARGs variation, succession and metabolism functions of bacterial communities when B&M processes were used for FW composting, suggesting a promising technology for reducing the transmission risk of ARGs and reaching maturity of FW composting.
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Affiliation(s)
- Xunan Li
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Panliang Wang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Siqin Chu
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Yulu Xu
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Yinglong Su
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Engineering Research Center for Nanophotonics and Advanced Instrument, Ministry of Education, East China Normal University, Shanghai 200062, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Dong Wu
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Engineering Research Center for Nanophotonics and Advanced Instrument, Ministry of Education, East China Normal University, Shanghai 200062, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Bing Xie
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Engineering Research Center for Nanophotonics and Advanced Instrument, Ministry of Education, East China Normal University, Shanghai 200062, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
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11
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Wang P, Yi Y, Lü X. CRISPR/Cas9-Based Genome Editing Platform for Companilactobacillus crustorum to Reveal the Molecular Mechanism of Its Probiotic Properties. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15279-15289. [PMID: 34747603 DOI: 10.1021/acs.jafc.1c05389] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Companilactobacillus crustorum usually serves as a starter culture for the food industry. Recent studies revealed that this species also possesses probiotic properties. Genome engineering, including point mutation or gene deletion, is desired to understand the mechanisms of its probiotic and fermentation properties. To tackle the hurdle in genetic manipulation in C. crustorum, here, we established a fast and easy CRISPR/Cas9-based platform for precise genome editing in this species. The platform includes two CRISPR/Cas9 systems and a CRISPR/Cas9-based editing system. Using the developed methods, we were able to knockout 12 genes in C. crustorum by deleting a fragment located in the open reading frames. The editing efficiency ranged from 14.3 to 100%. Moreover, we developed a CRISPR-assisted cytidine base-editing system, enabling programmed C to T conversion in the chromosome for gene inactivation or point mutation. To further exploit this platform, we investigated the role of nine putative bacteriocin-encoding genes and found that bacteriocins BM173 and BM1157 mostly contributed to the antimicrobial activity of C. crustorum MN047 against Staphylococcus aureus and Escherichia coli. In addition, the regulation of bacteriocin expression was also revealed to be linked with the quorum-sensing modulator luxS. This work will dramatically accelerate the genetic engineering of C. crustorum and close-related species.
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Affiliation(s)
- Panpan Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanglei Yi
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xin Lü
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
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Wang P, Wang T, Ismael M, Wang X, Yi Y, Lü X. Development of an electroporation method and expression patterns of bacteriocin-encoding genes in Companilactobacillus crustorum MN047. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Acetate Activates Lactobacillus Bacteriocin Synthesis by Controlling Quorum Sensing. Appl Environ Microbiol 2021; 87:e0072021. [PMID: 33893120 DOI: 10.1128/aem.00720-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bacteriocins are useful for controlling the composition of microorganisms in fermented food. Bacteriocin synthesis is regulated by quorum sensing mediated by autoinducing peptides. In addition, short-chain fatty acids, especially acetic acid, reportedly regulate bacteriocin synthesis. Five histidine kinases that regulated the synthesis of bacteriocins were selected to verify their interactions with acetate. Acetate activated the kinase activity of PlnB, SppK, and HpK3 in vitro and increased the yield of their cognate bacteriocins plantaricin EF, sakacin A, and rhamnosin B in vivo. The antimicrobial activity against Staphylococcus aureus of the fermentation supernatants of Lactobacillus plantarum, Lactobacillus sakei, and Lactobacillus rhamnosus with addition of acetate increased to 298%, 198%, and 289%, respectively, compared with that in the absence of acetate. Our study elucidated the activation activity of acetate in bacteriocin synthesis, and it might provide a potential strategy to increase the production of bacteriocin produced by Lactobacillus. IMPORTANCE Bacteriocins produced by lactic acid bacteria (LAB) are particularly useful in food preservation and food safety. Bacteriocins might increase bacterial competitive advantage against the indigenous microbiota of the intestines; at the same time, bacteriocins could limit the growth of undesired microorganisms in yogurt and other dairy products. This study confirmed that three kinds of histidine kinases were activated by acetate and upregulated bacteriocin synthesis both in vitro and in vivo. The increasing yield of bacteriocins reduced the number of pathogens and increased the number of probiotics in milk. Bacteriocin synthesis activation by acetate may have a broad application in the preservation of dairy products and forage silage.
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de Almeida OGG, Vitulo N, De Martinis ECP, Felis GE. Pangenome analyses of LuxS-coding genes and enzymatic repertoires in cocoa-related lactic acid bacteria. Genomics 2021; 113:1659-1670. [PMID: 33839269 DOI: 10.1016/j.ygeno.2021.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/04/2021] [Accepted: 04/05/2021] [Indexed: 01/15/2023]
Abstract
Lactobacillaceae presents potential for interspecific Quorum Sensing (QS) in spontaneous cocoa fermentation, correlated with high abundance of luxS. Three Brazilian isolates from cocoa fermentation were characterized by Whole Genome Sequencing and luxS gene was surveyed in their genomes, in comparison with public databases. They were classified as Lactiplantibacillus plantarum, Limosilactobacillus fermentum and Pediococcus acidilactici. LuxS genes were conserved in core genomes of the novel isolates, but in some non-cocoa related Lactic Acid Bacteria (LAB) it was accessory and plasmid-borne. The conservation and horizontal acquisition of luxS reinforces that QS is determinant for bacterial adaptation in several environments, especially taking into account the luxS has been correlated with modulation of bacteriocin production, stress tolerance and biofilm formation. Therefore, in this paper, new clade and species-specific primers were designed for future application for screening of luxS gene in LAB to evaluate the adaptive potential to diverse food fermentations.
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Affiliation(s)
| | - Nicola Vitulo
- University of Verona, Department of Biotechnology, Verona, Italy
| | | | - Giovanna E Felis
- University of Verona, Department of Biotechnology, Verona, Italy
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Wang L, Kong L, Hu X, Bai H, Wang Z, Jiang Y, Bi Y, Chang G, Chen G. Effect of stocking density on performance, meat quality and cecal bacterial communities of yellow feather broilers. Anim Biotechnol 2021; 33:1322-1332. [PMID: 33752552 DOI: 10.1080/10495398.2021.1898413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Totally, 315 42-day-old male Xueshan chickens were allocated into 3 caging densities, 14, 21 and 28 birds/m2. Each treatment was represented by 5 replicates. The body weight (BW), slaughter performance, meat quality, behavioral assessment, and the cecal microorganisms were detected at the market age. The results showed that the BW of broilers in the low- and medium-density groups was significantly higher (p < 0.05) than that of the high-density group from the age of 10 weeks. Only the feather quality of the broilers in the low-density group improved significantly (p < 0.05) compared with those of the other two groups. And, the abdominal fat percentage and the fat content of thigh muscle of broilers in the low- and medium-density groups were higher (p < 0.05) than those in the high-density group. No significant difference (p > 0.05) was noted in the other traits. The abundance of some microbial like Akkermansiaceae, Lactobacillaceae and Faecalibacterium may be correlated with the BW and fat content of broilers. The findings of this study suggest that increasing the stocking density decreased the final BW, fat content and the feather quality, whereas no evidence was found that stocking density caused changes in other parameters.
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Affiliation(s)
- Laidi Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Lingling Kong
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Xiaodan Hu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Zhixiu Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Yong Jiang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Yulin Bi
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guobin Chang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guohong Chen
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
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Emanuel E, Dubrovin I, Pogreb R, Pinhasi GA, Cahan R. Resuscitation of Pulsed Electric Field-Treated Staphylococcus aureus and Pseudomonas putida in a Rich Nutrient Medium. Foods 2021; 10:foods10030660. [PMID: 33808827 PMCID: PMC8003612 DOI: 10.3390/foods10030660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/04/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022] Open
Abstract
Pulsed electric fields (PEFs) technology was reported to be useful as a disinfection method in the liquid food industry. This technology may lead to membrane permeabilization and bacterial death. However, resuscitation of viable but non-culturable cells and sublethally injured microorganisms in food was reported to be associated with foodborne outbreaks. The main aim of this study was to investigate the possible recovery of injured PEF-treated bacteria. The PEF treatment of Staphylococcus aureus and Pseudomonas putida led to a reduction of 3.2 log10 and 4.8 log10, respectively. After 5 h, no colony forming units (CFUs) were observed when the bacteria were suspended in phosphate buffer saline (PBS); and for 24 h, no recovery was observed. The PEF-treated S. aureus in brain-heart infusion (BHI) medium were maintained at 1.84 × 104 CFU mL−1 for about 1.5 h. While P. putida decreased to zero CFU mL−1 by the 4th hour. However, after that, both bacteria recovered and began to multiply. Flow cytometry analysis showed that PEF treatment led to significant membrane permeabilization. Mass spectrometry analysis of PEF-treated P. putida which were suspended in BHI revealed over-expression of 22 proteins, where 55% were related to stress conditions. Understanding the recovery conditions of PEF-treated bacteria is particularly important in food industry pasteurization. To our knowledge, this is the first comprehensive study describing the recovery of injured PEF-treated S. aureus and P. putida bacteria.
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Affiliation(s)
- Efrat Emanuel
- Department of Chemical Engineering, Ariel University, Ariel 40700, Israel; (E.E.); (I.D.); (G.A.P.)
| | - Irina Dubrovin
- Department of Chemical Engineering, Ariel University, Ariel 40700, Israel; (E.E.); (I.D.); (G.A.P.)
| | - Roman Pogreb
- Department of Physics, Ariel University, Ariel 40700, Israel;
| | - Gad A. Pinhasi
- Department of Chemical Engineering, Ariel University, Ariel 40700, Israel; (E.E.); (I.D.); (G.A.P.)
| | - Rivka Cahan
- Department of Chemical Engineering, Ariel University, Ariel 40700, Israel; (E.E.); (I.D.); (G.A.P.)
- Correspondence: ; Tel.: +972-54-7740293
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Martínez B, Rodríguez A, Kulakauskas S, Chapot-Chartier MP. Cell wall homeostasis in lactic acid bacteria: threats and defences. FEMS Microbiol Rev 2021; 44:538-564. [PMID: 32495833 PMCID: PMC7476776 DOI: 10.1093/femsre/fuaa021] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 06/03/2020] [Indexed: 12/16/2022] Open
Abstract
Lactic acid bacteria (LAB) encompasses industrially relevant bacteria involved in food fermentations as well as health-promoting members of our autochthonous microbiota. In the last years, we have witnessed major progresses in the knowledge of the biology of their cell wall, the outermost macrostructure of a Gram-positive cell, which is crucial for survival. Sophisticated biochemical analyses combined with mutation strategies have been applied to unravel biosynthetic routes that sustain the inter- and intra-species cell wall diversity within LAB. Interplay with global cell metabolism has been deciphered that improved our fundamental understanding of the plasticity of the cell wall during growth. The cell wall is also decisive for the antimicrobial activity of many bacteriocins, for bacteriophage infection and for the interactions with the external environment. Therefore, genetic circuits involved in monitoring cell wall damage have been described in LAB, together with a plethora of defence mechanisms that help them to cope with external threats and adapt to harsh conditions. Since the cell wall plays a pivotal role in several technological and health-promoting traits of LAB, we anticipate that this knowledge will pave the way for the future development and extended applications of LAB.
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Affiliation(s)
- Beatriz Martínez
- DairySafe research group. Department of Technology and Biotechnology of Dairy Products. Instituto de Productos Lácteos de Asturias, IPLA-CSIC. Paseo Río Linares s/n. 33300 Villaviciosa, Spain
| | - Ana Rodríguez
- DairySafe research group. Department of Technology and Biotechnology of Dairy Products. Instituto de Productos Lácteos de Asturias, IPLA-CSIC. Paseo Río Linares s/n. 33300 Villaviciosa, Spain
| | - Saulius Kulakauskas
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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Leyva-Diaz AA, Hernandez-Patlan D, Solis-Cruz B, Adhikari B, Kwon YM, Latorre JD, Hernandez-Velasco X, Fuente-Martinez B, Hargis BM, Lopez-Arellano R, Tellez-Isaias G. Evaluation of curcumin and copper acetate against Salmonella Typhimurium infection, intestinal permeability, and cecal microbiota composition in broiler chickens. J Anim Sci Biotechnol 2021; 12:23. [PMID: 33541441 PMCID: PMC7863265 DOI: 10.1186/s40104-021-00545-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 01/04/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Interest in the use of natural feed additives as an alternative to antimicrobials in the poultry industry has increased in recent years because of the risk of bacterial resistance. One of the most studied groups are polyphenolic compounds, given their advantages over other types of additives and their easy potentiation of effects when complexes are formed with metal ions. Therefore, the objective of the present study was to evaluate the impact of dietary supplementation of copper acetate (CA), curcumin (CR), and their combination (CA-CR) against Salmonella Typhimurium colonization, intestinal permeability, and cecal microbiota composition in broiler chickens through a laboratory Salmonella infection model. S. Typhimurium recovery was determined on day 10 post-challenge by isolating Salmonella in homogenates of the right cecal tonsil (12 chickens per group) on Xylose Lysine Tergitol-4 (XLT-4) with novobiocin and nalidixic acid. Intestinal integrity was indirectly determined by the fluorometric measurement of fluorescein isothiocyanate dextran (FITC-d) in serum samples from blood obtained on d 10 post-S. Typhimurium challenge. Finally, microbiota analysis was performed using the content of the left caecal tonsil of 5 chickens per group by sequencing V4 region of 16S rRNA gene. RESULTS The results showed that in two independent studies, all experimental treatments were able to significantly reduce the S. Typhimurium colonization in cecal tonsils (CT, P < 0.0001) compared to the positive control (PC) group. However, only CA-CR was the most effective treatment in reducing S. Typhimurium counts in both independent studies. Furthermore, the serum fluorescein isothiocyanate dextran (FITC-d) concentration in chickens treated with CR was significantly lower when compared to PC (P = 0.0084), which is related to a decrease in intestinal permeability and therefore intestinal integrity. The effect of dietary treatments in reducing Salmonella was further supported by the analysis of 16S rRNA gene sequences using Linear discriminant analysis effect size (LEfSe) since Salmonella was significantly enriched in PC group (LDA score > 2.0 and P < 0.05) compared to other groups. In addition, Coprobacillus, Eubacterium, and Clostridium were significantly higher in the PC group compared to other treatment groups. On the contrary, Fecalibacterium and Enterococcus in CR, unknown genus of Erysipelotrichaceae at CA-CR, and unknown genus of Lachnospiraceae at CA were significantly more abundant respectively. CONCLUSIONS CR treatment was the most effective treatment to reduce S. Typhimurium intestinal colonization and maintain better intestinal homeostasis which might be achieved through modulation of cecal microbiota.
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Affiliation(s)
- Anaisa A. Leyva-Diaz
- Departamento de Medicina y Zootecnia de Aves, Facultad de Medicina Veterinaria y Zootecnia, UNAM, 04510 Ciudad de Mexico, Mexico
| | - Daniel Hernandez-Patlan
- Laboratorio 5: LEDEFAR, Unidad de Investigacion Multidisciplinaria, Facultad de Estudios Superiores (FES) Cuautitlan, Universidad Nacional Autonoma de Mexico (UNAM), 54714 Cuautitlan Izcalli, Mexico
| | - Bruno Solis-Cruz
- Laboratorio 5: LEDEFAR, Unidad de Investigacion Multidisciplinaria, Facultad de Estudios Superiores (FES) Cuautitlan, Universidad Nacional Autonoma de Mexico (UNAM), 54714 Cuautitlan Izcalli, Mexico
| | - Bishnu Adhikari
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, 1260 W. Maple, POSC 0-114, Fayetteville, AR 72704 USA
| | - Young Min Kwon
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, 1260 W. Maple, POSC 0-114, Fayetteville, AR 72704 USA
| | - Juan D. Latorre
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, 1260 W. Maple, POSC 0-114, Fayetteville, AR 72704 USA
| | - Xochitl Hernandez-Velasco
- Departamento de Medicina y Zootecnia de Aves, Facultad de Medicina Veterinaria y Zootecnia, UNAM, 04510 Ciudad de Mexico, Mexico
| | - Benjamin Fuente-Martinez
- Centro de Ensenanza, Investigacion y Extension en Produccion Avicola, Facultad de Medicina Veterinaria y Zootecnia, UNAM, Ciudad de Mexico, Mexico
| | - Billy M. Hargis
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, 1260 W. Maple, POSC 0-114, Fayetteville, AR 72704 USA
| | - Raquel Lopez-Arellano
- Laboratorio 5: LEDEFAR, Unidad de Investigacion Multidisciplinaria, Facultad de Estudios Superiores (FES) Cuautitlan, Universidad Nacional Autonoma de Mexico (UNAM), 54714 Cuautitlan Izcalli, Mexico
| | - Guillermo Tellez-Isaias
- Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, 1260 W. Maple, POSC 0-114, Fayetteville, AR 72704 USA
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Chi Y, Ren T, Shi X, Jin X, Jin P. Mechanism of nutrient removal enhancement in low carbon/nitrogen wastewater by a novel high-frequency micro-aeration/anoxic (HMOA) mode. CHEMOSPHERE 2021; 263:128003. [PMID: 33297037 DOI: 10.1016/j.chemosphere.2020.128003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 05/26/2023]
Abstract
In this study, a novel high-frequency micro-aeration/anoxic (HMOA) mode with a high aeration frequency (15 times/h) and short aeration duration (Taer = 1 h/cycle) was proposed. Compared with continuous aeration modes, the highest nitrogen and phosphorus removal efficiencies were achieved in the sequencing batch reactor (SBR) under HMOA mode when treating wastewater with carbon/nitrogen (C/N) ratios of 4.5 (85% and 97%, respectively) and 3 (77% and 75%, respectively). Metagenomic analysis was utilized to analyse the microbial metabolic mechanism under the HMOA mode. The results showed that under the HMOA mode, the enhanced transduction and metabolism pathways of nitrate, nitrite, oxygen, phosphorus and acetate provided favourable nutritional conditions for the proliferation of denitrifiers and phosphorus accumulating organisms (PAOs), and simultaneously strengthened the survival capacity of nitrifiers under low dissolved oxygen (DO) conditions. In addition, genes involved in carbon metabolism were upregulated by the HMOA mode, which further increased the utility of carbon sources for denitrifier and PAO metabolism. Consequently, the limited carbon source could be fully utilized in nitrogen and phosphorus removal, which improved the efficiency of treating low C/N wastewater. This study proposed a potential aeration mode for microbial metabolism regulation to enhance nutrient removal in biological wastewater treatment processes.
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Affiliation(s)
- Yulei Chi
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and, Technology, Xi'an, Shaanxi Province, 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture, and Technology, Xi'an, Shaanxi Province, 710055, China
| | - Tong Ren
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and, Technology, Xi'an, Shaanxi Province, 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture, and Technology, Xi'an, Shaanxi Province, 710055, China
| | - Xuan Shi
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and, Technology, Xi'an, Shaanxi Province, 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture, and Technology, Xi'an, Shaanxi Province, 710055, China
| | - Xin Jin
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and, Technology, Xi'an, Shaanxi Province, 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture, and Technology, Xi'an, Shaanxi Province, 710055, China
| | - Pengkang Jin
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and, Technology, Xi'an, Shaanxi Province, 710055, China; Northwest China Key Laboratory of Water Resources and Environment Ecology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China.
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Metagenomic insights into the changes in microbial community and antimicrobial resistance genes associated with different salt content of red pepper (Capsicum annuum L.) sauce. Food Microbiol 2020; 85:103295. [DOI: 10.1016/j.fm.2019.103295] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/03/2019] [Accepted: 08/07/2019] [Indexed: 01/06/2023]
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21
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Measures to improve wine malolactic fermentation. Appl Microbiol Biotechnol 2019; 103:2033-2051. [DOI: 10.1007/s00253-018-09608-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 12/27/2018] [Indexed: 01/06/2023]
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Mazhar S, Hill C, McAuliffe O. The Genus Macrococcus: An Insight Into Its Biology, Evolution, and Relationship With Staphylococcus. ADVANCES IN APPLIED MICROBIOLOGY 2018; 105:1-50. [PMID: 30342720 DOI: 10.1016/bs.aambs.2018.05.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The Gram-positive genus Macrococcus is composed of eight species that are evolutionarily closely related to species of the Staphylococcus genus. In contrast to Staphylococcus species, species of Macrococcus are generally regarded to be avirulent in their animal hosts. Recent reports on Macrococcus have focused on the presence of novel methicillin resistance genes in Macrococcus caseolyticus and Macrococcus canis, with the discovery of the first plasmid-encoded methicillin resistance gene in clinical Staphylococcus aureus of probable macrococcal origin generating further interest in these organisms. Furthermore, M. caseolyticus has been associated with flavor development in certain fermented foods and its potential as a food bio-preservative has been documented. The potential application of these organisms in food seems at odds with the emerging information regarding antibiotic resistance and is prompting further examination of the potential safety issues associated with such strains, given the European Food Safety Authority framework for the safety evaluation of microorganisms in the food chain. A comprehensive understanding of the genus would also contribute to understanding the evolution of staphylococci in terms of its acquisition of antibiotic resistance and pathogenic potential. In this review, we discuss the current knowledge on Macrococcus with regard to their phenotypic capabilities, genetic diversity, and evolutionary history with Staphylococcus. Comparative genomics of the sequenced Macrococcus species will be discussed, providing insight into their unique metabolic features and the genetic structures carrying methicillin resistance. An in-depth understanding of these antibiotic resistance determinants can open the possibilities for devising better preventative strategies for an unpredictable future.
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Affiliation(s)
- Shahneela Mazhar
- Teagasc Food Research Centre, Moorepark, Fermoy, Co., Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Olivia McAuliffe
- Teagasc Food Research Centre, Moorepark, Fermoy, Co., Cork, Ireland
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Chia LW, Hornung BVH, Aalvink S, Schaap PJ, de Vos WM, Knol J, Belzer C. Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach. Antonie Van Leeuwenhoek 2018; 111:859-873. [PMID: 29460206 PMCID: PMC5945754 DOI: 10.1007/s10482-018-1040-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 02/02/2018] [Indexed: 12/26/2022]
Abstract
Host glycans are paramount in regulating the symbiotic relationship between humans and their gut bacteria. The constant flux of host-secreted mucin at the mucosal layer creates a steady niche for bacterial colonization. Mucin degradation by keystone species subsequently shapes the microbial community. This study investigated the transcriptional response during mucin-driven trophic interaction between the specialised mucin-degrader Akkermansia muciniphila and a butyrogenic gut commensal Anaerostipes caccae. A. muciniphila monocultures and co-cultures with non-mucolytic A. caccae from the Lachnospiraceae family were grown anaerobically in minimal media supplemented with mucin. We analysed for growth, metabolites (HPLC analysis), microbial composition (quantitative reverse transcription PCR), and transcriptional response (RNA-seq). Mucin degradation by A. muciniphila supported the growth of A. caccae and concomitant butyrate production predominantly via the acetyl-CoA pathway. Differential expression analysis (DESeq 2) showed the presence of A. caccae induced changes in the A. muciniphila transcriptional response with increased expression of mucin degradation genes and reduced expression of ribosomal genes. Two putative operons that encode for uncharacterised proteins and an efflux system, and several two-component systems were also differentially regulated. This indicated A. muciniphila changed its transcriptional regulation in response to A. caccae. This study provides insight to understand the mucin-driven microbial ecology using metatranscriptomics. Our findings show that the expression of mucolytic enzymes by A. muciniphila increases upon the presence of a community member. This could indicate its role as a keystone species that supports the microbial community in the mucosal environment by increasing the availability of mucin sugars.
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Affiliation(s)
- Loo Wee Chia
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Bastian V H Hornung
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Steven Aalvink
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- RPU Immunobiology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, 00290, Helsinki, Finland
| | - Jan Knol
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- Nutricia Research, Uppsalalaan 12, 3584 CT, Utrecht, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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Arnold JW, Simpson JB, Roach J, Kwintkiewicz J, Azcarate-Peril MA. Intra-species Genomic and Physiological Variability Impact Stress Resistance in Strains of Probiotic Potential. Front Microbiol 2018; 9:242. [PMID: 29515537 PMCID: PMC5826259 DOI: 10.3389/fmicb.2018.00242] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/31/2018] [Indexed: 12/28/2022] Open
Abstract
Large-scale microbiome studies have established that most of the diversity contained in the gastrointestinal tract is represented at the strain level; however, exhaustive genomic and physiological characterization of human isolates is still lacking. With increased use of probiotics as interventions for gastrointestinal disorders, genomic and functional characterization of novel microorganisms becomes essential. In this study, we explored the impact of strain-level genomic variability on bacterial physiology of two novel human Lactobacillus rhamnosus strains (AMC143 and AMC010) of probiotic potential in relation to stress resistance. The strains showed differences with known probiotic strains (L. rhamnosus GG, Lc705, and HN001) at the genomic level, including nucleotide polymorphisms, mutations in non-coding regulatory regions, and rearrangements of genomic architecture. Transcriptomics analysis revealed that gene expression profiles differed between strains when exposed to simulated gastrointestinal stresses, suggesting the presence of unique regulatory systems in each strain. In vitro physiological assays to test resistance to conditions mimicking the gut environment (acid, alkali, and bile stress) showed that growth of L. rhamnosus AMC143 was inhibited upon exposure to alkaline pH, while AMC010 and control strain LGG were unaffected. AMC143 also showed a significant survival advantage compared to the other strains upon bile exposure. Reverse transcription qPCR targeting the bile salt hydrolase gene (bsh) revealed that AMC143 expressed bsh poorly (a consequence of a deletion in the bsh promoter and truncation of bsh gene in AMC143), while AMC010 had significantly higher expression levels than AMC143 or LGG. Insertional inactivation of the bsh gene in AMC010 suggested that bsh could be detrimental to bacterial survival during bile stress. Together, these findings show that coupling of classical microbiology with functional genomics methods for the characterization of bacterial strains is critical for the development of novel probiotics, as variability between strains can dramatically alter bacterial physiology and functionality.
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Affiliation(s)
- Jason W. Arnold
- Division of Gastroenterology and Hepatology, Department of Medicine, Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Joshua B. Simpson
- Department of Chemistry, College of Arts and Sciences, University of North Carolina, Chapel Hill, NC, United States
| | - Jeffrey Roach
- Research Computing, University of North Carolina, Chapel Hill, NC, United States
| | - Jakub Kwintkiewicz
- Division of Gastroenterology and Hepatology, Department of Medicine, Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - M. Andrea Azcarate-Peril
- Division of Gastroenterology and Hepatology, Department of Medicine, Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
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