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Coltman BL, Rebnegger C, Gasser B, Zanghellini J. Characterising the metabolic rewiring of extremely slow growing Komagataella phaffii. Microb Biotechnol 2024; 17:e14386. [PMID: 38206275 PMCID: PMC10832545 DOI: 10.1111/1751-7915.14386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 01/12/2024] Open
Abstract
Retentostat cultivations have enabled investigations into substrate-limited near-zero growth for a number of microbes. Quantitative physiology at these near-zero growth conditions has been widely discussed, yet characterisation of the fluxome is relatively under-reported. We investigated the rewiring of metabolism in the transition of a recombinant protein-producing strain of Komagataella phaffii to glucose-limited near-zero growth rates. We used cultivation data from a 200-fold range of growth rates and comprehensive biomass composition data to integrate growth rate dependent biomass equations, generated using a number of different approaches, into a K. phaffii genome-scale metabolic model. Here, we show that a non-growth-associated maintenance value of 0.65 mmol ATP g CDW - 1 h - 1 and a growth-associated maintenance value of 108 mmol ATP g CDW - 1 lead to accurate growth rate predictions. In line with its role as energy source, metabolism is rewired to increase the yield of ATP per glucose. This includes a reduction of flux through the pentose phosphate pathway, and a greater utilisation of glycolysis and the TCA cycle. Interestingly, we observed activity of an external, non-proton translocating NADH dehydrogenase in addition to the malate-aspartate shuttle. Regardless of the method used for the generation of biomass equations, a similar, yet different, growth rate dependent rewiring was predicted. As expected, these differences between the different methods were clearer at higher growth rates, where the biomass equation provides a much greater constraint than at slower growth rates. When placed on an increasingly limited glucose diet, the metabolism of K. phaffii adapts, enabling it to continue to drive critical processes sustaining its high viability at near-zero growth rates.
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Affiliation(s)
- Benjamin Luke Coltman
- CD‐Laboratory for Growth‐decoupled Protein Production in Yeast at Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Department of Biotechnology, Institute of Microbiology and Microbial BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Corinna Rebnegger
- CD‐Laboratory for Growth‐decoupled Protein Production in Yeast at Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Department of Biotechnology, Institute of Microbiology and Microbial BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Brigitte Gasser
- CD‐Laboratory for Growth‐decoupled Protein Production in Yeast at Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Department of Biotechnology, Institute of Microbiology and Microbial BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Jürgen Zanghellini
- Austrian Centre of Industrial BiotechnologyViennaAustria
- Department of Analytical ChemistryUniversity of ViennaViennaAustria
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2
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Ortiz Camargo AR, van Mastrigt O, Bongers RS, Ben-Amor K, Knol J, Abee T, Smid EJ. Quantitative Physiology and Proteome Adaptations of Bifidobacterium breve NRBB57 at Near-Zero Growth Rates. Microbiol Spectr 2023; 11:e0256822. [PMID: 37184421 PMCID: PMC10269484 DOI: 10.1128/spectrum.02568-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 04/26/2023] [Indexed: 05/16/2023] Open
Abstract
In natural environments, nutrients are usually scarce, causing microorganisms to grow slowly while staying metabolically active. These natural conditions can be simulated using retentostat cultivations. The present study describes the physiological and proteome adaptations of the probiotic Bifidobacterium breve NRBB57 from high (0.4 h-1) to near-zero growth rates. Lactose-limited retentostat cultivations were carried out for 21 days in which the bacterial growth rate progressively reduced to 0.00092 h-1, leading to a 3.4-fold reduction of the maintenance energy requirement. Lactose was mainly converted into acetate, formate, and ethanol at high growth rates, while in the retentostat, lactate production increased. Interestingly, the consumption of several amino acids (serine, aspartic acid, and glutamine/arginine) and glycerol increased over time in the retentostat. Morphological changes and viable but nonculturable cells were also observed in the retentostat. Proteomes were compared for all growth rates, revealing a downregulation of ribosomal proteins at near-zero growth rates and an upregulation of proteins involved in the catabolism of alternative energy sources. Finally, we observed induction of the stringent response and stress defense systems. Retentostat cultivations were proven useful to study the physiology of B. breve, mimicking the nutrient scarcity of its complex habitat, the human gut. IMPORTANCE In natural environments, nutrients are usually scarce, causing microorganisms to grow slowly while staying metabolically active. In this study we used retentostat cultivation to investigate how the probiotic Bifidobacterium breve adapts its physiology and proteome under severe nutrient limitation resulting in near-zero growth rates (<0.001 h-1). We showed that the nutrient limitation induced a multifaceted response including stress defense and stringent response, metabolic shifts, and the activation of novel alternative energy-producing pathways.
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Affiliation(s)
| | - Oscar van Mastrigt
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | | | | | - Jan Knol
- Danone Nutricia Research, Utrecht, The Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Eddy J. Smid
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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3
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Jang HY, Kim MJ, Bae M, Hwang IM, Lee JH. Transcriptional analysis of the molecular mechanism underlying the response of Lactiplantibacillus plantarum to lactic acid stress conditions. Heliyon 2023; 9:e16520. [PMID: 37303574 PMCID: PMC10250755 DOI: 10.1016/j.heliyon.2023.e16520] [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: 12/07/2022] [Revised: 05/02/2023] [Accepted: 05/19/2023] [Indexed: 06/13/2023] Open
Abstract
Lactic acid bacteria (LAB) present various benefits to humans; they play key roles in the fermentation of food and as probiotics. Acidic conditions are common to both LAB in the intestinal tract as well as fermented foods. Lactiplantibacillus plantarum is a facultative homofermentative bacterium, and lactic acid is the end metabolite of glycolysis. To characterize how L. plantarum responds to lactic acid, we investigated its transcriptome following treatment with hydrochloride (HCl) or dl-lactic acid at an early stage of growth. Bacterial growth was more attenuated in the presence of lactic acid than in the presence of HCl at the same pH range. Bacterial transcriptome analysis showed that the expression of 67 genes was significantly altered (log2FC > 2 or < 2). A total of 31 genes were up- or downregulated under both conditions: 19 genes in the presence of HCl and 17 genes in the presence of dl-lactic acid. The fatty acid synthesis-related genes were upregulated in both acidic conditions, whereas the lactate racemization-related gene (lar) was only upregulated following treatment with dl-lactic acid. In particular, lar expression increased following l-lactic acid treatment but did not increase following HCl or d-lactic acid treatment. Expression of lar and production of d-lactic acid were investigated with malic and acetic acid; the results revealed a higher expression of lar and production of d-lactic acid in the presence of malic acid than that in the presence of acetic acid.
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4
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Camargo ARO, Van Mastrigt O, Bongers RS, Ben-Amor K, Knol J, Smid EJ, Abee T. Enhanced stress resistance of Bifidobacterium breve NRBB57 by induction of stress proteins at near-zero growth rates. Benef Microbes 2023; 14:85-94. [PMID: 36790092 DOI: 10.3920/bm2022.0074] [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: 02/16/2023]
Abstract
Bifidobacterium breve is a common habitant of the human gut and is used as probiotic in functional foods. B. breve has to cope with multiple stress conditions encountered during processing and passage through the human gut, including high temperature, low pH and exposure to oxygen. Additionally, during industrial processing and in the gut, B. breve could encounter nutrient limitation resulting in reduced growth rates that can trigger adaptive stress responses. For this reason, it is important to develop culture methods that elicit resistance to multiple stresses (robustness) encountered by the bacteria. To investigate the impact of caloric restriction on robustness of the probiotic B. breve NRBB57, this strain was grown in lactose-limited chemostat cultures and in retentostat for 21 days, at growth rates ranging from 0.4 h-1 to 0.00081 h-1. Proteomes of cells harvested at different growth rates were correlated to acid, hydrogen peroxide and heat stress survival capacity. Comparative proteome analysis showed that retentostat-grown cells had significantly increased abundance of a variety of stress proteins involved in protein quality maintenance and DNA repair (DnaJ, Hsp90, FtsH, ClpB, ClpP1, ClpC, GroES, RuvB, RecA), as well as proteins involved in oxidative stress defence (peroxiredoxin, ferredoxin, thioredoxin peroxidase, glutaredoxin and thioredoxin reductase). Exposure to three different stress conditions, 45 °C, pH 3, and 10 mM H2O2, showed highest stress resistance of retentostat cells sampled at week 2 and week 3 grown at 0.0018 and 0.00081 h-1. Our findings show that cultivation at near-zero growth rates induces higher abundance of stress defence proteins contributing to the robustness of B. breve NRBB57, thereby offering an approach that may support its production and functionality.
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Affiliation(s)
- A R Ortiz Camargo
- Food Microbiology, Wageningen University & Research, P.O. box 17, 6700 AA Wageningen, The Netherlands
| | - O Van Mastrigt
- Food Microbiology, Wageningen University & Research, P.O. box 17, 6700 AA Wageningen, The Netherlands
| | - R S Bongers
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT Utrecht, the Netherlands
| | - K Ben-Amor
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT Utrecht, the Netherlands
| | - J Knol
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT Utrecht, the Netherlands.,Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH Wageningen, the Netherlands
| | - E J Smid
- Food Microbiology, Wageningen University & Research, P.O. box 17, 6700 AA Wageningen, The Netherlands
| | - T Abee
- Food Microbiology, Wageningen University & Research, P.O. box 17, 6700 AA Wageningen, The Netherlands
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5
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Jaffar NS, Jawan R, Chong KP. The potential of lactic acid bacteria in mediating the control of plant diseases and plant growth stimulation in crop production - A mini review. FRONTIERS IN PLANT SCIENCE 2023; 13:1047945. [PMID: 36714743 PMCID: PMC9880282 DOI: 10.3389/fpls.2022.1047945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/27/2022] [Indexed: 06/18/2023]
Abstract
The microbial diseases cause significant damage in agriculture, resulting in major yield and quality losses. To control microbiological damage and promote plant growth, a number of chemical control agents such as pesticides, herbicides, and insecticides are available. However, the rising prevalence of chemical control agents has led to unintended consequences for agricultural quality, environmental devastation, and human health. Chemical agents are not naturally broken down by microbes and can be found in the soil and environment long after natural decomposition has occurred. As an alternative to chemical agents, biocontrol agents are employed to manage phytopathogens. Interest in lactic acid bacteria (LAB) research as another class of potentially useful bacteria against phytopathogens has increased in recent years. Due to the high level of biosafety, they possess and the processes they employ to stimulate plant growth, LAB is increasingly being recognized as a viable option. This paper will review the available information on the antagonistic and plant-promoting capabilities of LAB and its mechanisms of action as well as its limitation as BCA. This review aimed at underlining the benefits and inputs from LAB as potential alternatives to chemical usage in sustaining crop productivity.
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Affiliation(s)
- Nur Sulastri Jaffar
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Sabah, Malaysia
- Horticulture Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), Selangor, Malaysia
| | - Roslina Jawan
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Sabah, Malaysia
| | - Khim Phin Chong
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Sabah, Malaysia
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6
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Tang Z, Zhao Z, Wu X, Lin W, Qin Y, Chen H, Wan Y, Zhou C, Bu T, Chen H, Xiao Y. A Review on Fruit and Vegetable Fermented Beverage-Benefits of Microbes and Beneficial Effects. FOOD REVIEWS INTERNATIONAL 2022. [DOI: 10.1080/87559129.2021.2024222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Zizhong Tang
- College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Zhiqiao Zhao
- College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Xulong Wu
- Chengdu Agricultural College, Chengdu, Sichuan, China
| | - Wenjie Lin
- College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Yihan Qin
- College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Hui Chen
- College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Yujun Wan
- Sichuan Food and Fermentation Industry Research and Design Institute, Chengdu,Sichuan, China
| | - Caixia Zhou
- College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Tongliang Bu
- College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Hong Chen
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Yirong Xiao
- Sichuan Agricultural University Hospital, Ya’an, Sichuan, China
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7
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Douwenga S, Janssen P, Teusink B, Bachmann H. A centrifugation-based clearing method allows high-throughput acidification and growth-rate measurements in milk. J Dairy Sci 2021; 104:8530-8540. [PMID: 33934870 DOI: 10.3168/jds.2020-20108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/25/2021] [Indexed: 11/19/2022]
Abstract
The turbidity of milk prohibits the use of optical density measurements for strain characterizations. This often limits research to laboratory media. Here, we cleared milk through centrifugation to remove insoluble milk solids. This resulted in a clear liquid phase, termed milk serum, in which optical density measurements can be used to track microbial growth until a pH of 5.2 is reached. At pH 5.2 coagulation of the soluble protein occurs, making the medium opaque again. We found that behavior in milk serum was predictive of that in milk for 39 Lactococcus lactis (R2 = 0.81) and to a lesser extent for 42 Lactiplantibacillus plantarum (formerly Lactobacillus plantarum; R2 = 0.49) strains. Hence, milk serum can be used as an optically clear alternative to milk for comparison of microbial growth and metabolic characteristics. Characterization of the growth rate, specific acidification rate for optical density at a wavelength of 600 nm, and the amount of acid produced per unit of biomass for all these strains in milk serum, showed that almost all strains could grow in milk, with higher specific acidification and growth rates of Lc. lactis strains compared with Lb. plantarum strains. Nondairy Lc. lactis isolates had a lower growth and specific acidification rate than dairy isolates. The amount of acid produced per unit biomass was relatively high and similar for Lc. lactis dairy and nondairy isolates, as opposed to Lb. plantarum isolates. Lactococcus lactis ssp. lactis showed slightly lower growth and acidification rates when compared with ssp. cremoris. For Lc. lactis strains a doubling of the specific acidification rate occurred with a doubling of the maximum growth rate. This relation was not found for Lb. plantarum strains, where the acidification rate remained relatively constant across 39 strains with growth rates ranging from 0.2 h-1 to 0.3 h-1. We conclude that milk serum is a valuable alternative to milk for high-throughput strain characterization during milk fermentation.
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Affiliation(s)
- Sieze Douwenga
- TI Food and Nutrition, 6709 PA, Wageningen, the Netherlands; Systems Biology Lab, Vrije Universiteit Amsterdam, 1081 HZ, Amsterdam, the Netherlands
| | - Patrick Janssen
- TI Food and Nutrition, 6709 PA, Wageningen, the Netherlands; Health Department, NIZO Food Research, 6718 ZB, Ede, the Netherlands
| | - Bas Teusink
- TI Food and Nutrition, 6709 PA, Wageningen, the Netherlands; Systems Biology Lab, Vrije Universiteit Amsterdam, 1081 HZ, Amsterdam, the Netherlands
| | - Herwig Bachmann
- TI Food and Nutrition, 6709 PA, Wageningen, the Netherlands; Systems Biology Lab, Vrije Universiteit Amsterdam, 1081 HZ, Amsterdam, the Netherlands; Health Department, NIZO Food Research, 6718 ZB, Ede, the Netherlands.
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8
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An alternative resource allocation strategy in the chemolithoautotrophic archaeon Methanococcus maripaludis. Proc Natl Acad Sci U S A 2021; 118:2025854118. [PMID: 33879571 DOI: 10.1073/pnas.2025854118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Most microorganisms in nature spend the majority of time in a state of slow or zero growth and slow metabolism under limited energy or nutrient flux rather than growing at maximum rates. Yet, most of our knowledge has been derived from studies on fast-growing bacteria. Here, we systematically characterized the physiology of the methanogenic archaeon Methanococcus maripaludis during slow growth. M. maripaludis was grown in continuous culture under energy (formate)-limiting conditions at different dilution rates ranging from 0.09 to 0.002 h-1, the latter corresponding to 1% of its maximum growth rate under laboratory conditions (0.23 h-1). While the specific rate of methanogenesis correlated with growth rate as expected, the fraction of cellular energy used for maintenance increased and the maintenance energy per biomass decreased at slower growth. Notably, proteome allocation between catabolic and anabolic pathways was invariant with growth rate. Unexpectedly, cells maintained their maximum methanogenesis capacity over a wide range of growth rates, except for the lowest rates tested. Cell size, cellular DNA, RNA, and protein content as well as ribosome numbers also were largely invariant with growth rate. A reduced protein synthesis rate during slow growth was achieved by a reduction in ribosome activity rather than via the number of cellular ribosomes. Our data revealed a resource allocation strategy of a methanogenic archaeon during energy limitation that is fundamentally different from commonly studied versatile chemoheterotrophic bacteria such as E. coli.
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9
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Kleerebezem M, Bachmann H, van Pelt-KleinJan E, Douwenga S, Smid EJ, Teusink B, van Mastrigt O. Lifestyle, metabolism and environmental adaptation in Lactococcus lactis. FEMS Microbiol Rev 2021; 44:804-820. [PMID: 32990728 DOI: 10.1093/femsre/fuaa033] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/28/2020] [Indexed: 12/14/2022] Open
Abstract
Lactococcus lactis serves as a paradigm organism for the lactic acid bacteria (LAB). Extensive research into the molecular biology, metabolism and physiology of several model strains of this species has been fundamental for our understanding of the LAB. Genomic studies have provided new insights into the species L. lactis, including the resolution of the genetic basis of its subspecies division, as well as the control mechanisms involved in the fine-tuning of growth rate and energy metabolism. In addition, it has enabled novel approaches to study lactococcal lifestyle adaptations to the dairy application environment, including its adjustment to near-zero growth rates that are particularly relevant in the context of cheese ripening. This review highlights various insights in these areas and exemplifies the strength of combining experimental evolution with functional genomics and bacterial physiology research to expand our fundamental understanding of the L. lactis lifestyle under different environmental conditions.
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Affiliation(s)
- Michiel Kleerebezem
- Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University, De Elst 1, 6708 WD Wageningen, the Netherlands
| | - Herwig Bachmann
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.,NIZO food research, Kernhemseweg 2, 6718 ZB Ede, the Netherlands
| | - Eunice van Pelt-KleinJan
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.,TiFN Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen, the Netherlands
| | - Sieze Douwenga
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.,TiFN Food & Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen, the Netherlands
| | - Eddy J Smid
- Laboratory of Food Microbiology, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Bas Teusink
- Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - Oscar van Mastrigt
- Laboratory of Food Microbiology, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
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10
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Effect of hydrogen peroxide on the dehydrogenase and quinone-reductase activity of irradiated Lactobacillus plantarum cells. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.110236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Marinos G, Kaleta C, Waschina S. Defining the nutritional input for genome-scale metabolic models: A roadmap. PLoS One 2020; 15:e0236890. [PMID: 32797084 PMCID: PMC7428157 DOI: 10.1371/journal.pone.0236890] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/15/2020] [Indexed: 12/13/2022] Open
Abstract
The reconstruction and application of genome-scale metabolic network models is a central topic in the field of systems biology with numerous applications in biotechnology, ecology, and medicine. However, there is no agreed upon standard for the definition of the nutritional environment for these models. The objective of this article is to provide a guideline and a clear paradigm on how to translate nutritional information into an in-silico representation of the chemical environment. Step-by-step procedures explain how to characterise and categorise the nutritional input and to successfully apply it to constraint-based metabolic models. In parallel, we illustrate the proposed procedure with a case study of the growth of Escherichia coli in a complex nutritional medium and show that an accurate representation of the medium is crucial for physiological predictions. The proposed framework will assist researchers to expand their existing metabolic models of their microbial systems of interest with detailed representations of the nutritional environment, which allows more accurate and reproducible predictions of microbial metabolic processes.
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Affiliation(s)
- Georgios Marinos
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, University Medical Center Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, University Medical Center Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Silvio Waschina
- Division of Nutriinformatics, Institute for Human Nutrition and Food Sciences, Kiel University, Kiel, Schleswig-Holstein, Germany
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12
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Moens E, Bolca S, Possemiers S, Verstraete W. A Wake-Up Call for the Efficient Use of the Bacterial Resting Cell Process, with Focus on Low Solubility Products. Curr Microbiol 2020; 77:1349-1362. [PMID: 32270205 DOI: 10.1007/s00284-020-01959-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/21/2020] [Indexed: 11/24/2022]
Abstract
Micro-organisms are often subjected to stressful conditions. Owing to their capacity to adapt, they try to rapidly cope with the unfavorable conditions by lowering their growth rate, changing their morphology, and developing altered metabolite production and other stress-related metabolism. The stress-related metabolism of the cells which interrupted their growth is often referred to as resting metabolism and can be exploit for specific and high rate production of secondary metabolites. Although the bacterial resting cell process has been described decades ago, we find it worthwhile to bring the process under renewed attention and refer to this type of processes as non-growing metabolically active (NGMA) cell processes. Despite their use may sound counterproductive, NGMA cells can be of interest to increase substrate conversion rates or enable conversion of certain substrates, not accessible to growing cells due to their bacteriostatic nature or requirement of resistance to a multitude of different stress mechanisms. Biomass reuse is an interesting feature to improve the economics of NGMA cell processes. Yet, for lipophilic compounds or compounds with low solubility, biomass separation can be delicate. This review draws the attention on existing examples of NGMA cell processes, summarizing some developmental tools and highlighting drawbacks and opportunities, to answer the research question if NGMA cells can have a distinct added value in industry. Particular elaboration is made on a novel and more broadly applicable strategy to enable biomass reuse for conversions of compounds with low solubility.
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Affiliation(s)
- Esther Moens
- ProDigest BVBA, Technol Pk 82, 9052, Ghent, Belgium
| | - Selin Bolca
- ProDigest BVBA, Technol Pk 82, 9052, Ghent, Belgium
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13
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Consuegra J, Grenier T, Baa-Puyoulet P, Rahioui I, Akherraz H, Gervais H, Parisot N, da Silva P, Charles H, Calevro F, Leulier F. Drosophila-associated bacteria differentially shape the nutritional requirements of their host during juvenile growth. PLoS Biol 2020; 18:e3000681. [PMID: 32196485 PMCID: PMC7112240 DOI: 10.1371/journal.pbio.3000681] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 04/01/2020] [Accepted: 03/04/2020] [Indexed: 01/14/2023] Open
Abstract
The interplay between nutrition and the microbial communities colonizing the gastrointestinal tract (i.e., gut microbiota) determines juvenile growth trajectory. Nutritional deficiencies trigger developmental delays, and an immature gut microbiota is a hallmark of pathologies related to childhood undernutrition. However, how host-associated bacteria modulate the impact of nutrition on juvenile growth remains elusive. Here, using gnotobiotic Drosophila melanogaster larvae independently associated with Acetobacter pomorumWJL (ApWJL) and Lactobacillus plantarumNC8 (LpNC8), 2 model Drosophila-associated bacteria, we performed a large-scale, systematic nutritional screen based on larval growth in 40 different and precisely controlled nutritional environments. We combined these results with genome-based metabolic network reconstruction to define the biosynthetic capacities of Drosophila germ-free (GF) larvae and its 2 bacterial partners. We first established that ApWJL and LpNC8 differentially fulfill the nutritional requirements of the ex-GF larvae and parsed such difference down to individual amino acids, vitamins, other micronutrients, and trace metals. We found that Drosophila-associated bacteria not only fortify the host’s diet with essential nutrients but, in specific instances, functionally compensate for host auxotrophies by either providing a metabolic intermediate or nutrient derivative to the host or by uptaking, concentrating, and delivering contaminant traces of micronutrients. Our systematic work reveals that beyond the molecular dialogue engaged between the host and its bacterial partners, Drosophila and its associated bacteria establish an integrated nutritional network relying on nutrient provision and utilization. A study of gnotobiotic fruit flies shows that the animal is involved in an integrated nutritional network with its facultative commensal bacteria, centered around the utilization and sharing of nutrients.
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Affiliation(s)
- Jessika Consuegra
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, Lyon, France
| | - Théodore Grenier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, Lyon, France
| | - Patrice Baa-Puyoulet
- Laboratoire Biologie Fonctionnelle, Insectes et Interactions, Université de Lyon, Institut National des Sciences Appliquées, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, UMR0203, Villeurbanne, France
| | - Isabelle Rahioui
- Laboratoire Biologie Fonctionnelle, Insectes et Interactions, Université de Lyon, Institut National des Sciences Appliquées, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, UMR0203, Villeurbanne, France
| | - Houssam Akherraz
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, Lyon, France
| | - Hugo Gervais
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, Lyon, France
| | - Nicolas Parisot
- Laboratoire Biologie Fonctionnelle, Insectes et Interactions, Université de Lyon, Institut National des Sciences Appliquées, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, UMR0203, Villeurbanne, France
| | - Pedro da Silva
- Laboratoire Biologie Fonctionnelle, Insectes et Interactions, Université de Lyon, Institut National des Sciences Appliquées, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, UMR0203, Villeurbanne, France
| | - Hubert Charles
- Laboratoire Biologie Fonctionnelle, Insectes et Interactions, Université de Lyon, Institut National des Sciences Appliquées, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, UMR0203, Villeurbanne, France
| | - Federica Calevro
- Laboratoire Biologie Fonctionnelle, Insectes et Interactions, Université de Lyon, Institut National des Sciences Appliquées, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, UMR0203, Villeurbanne, France
| | - François Leulier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, Lyon, France
- * E-mail:
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14
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Yu AO, Leveau JHJ, Marco ML. Abundance, diversity and plant-specific adaptations of plant-associated lactic acid bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:16-29. [PMID: 31573142 DOI: 10.1111/1758-2229.12794] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
Lactic acid bacteria (LAB) are essential for many fruit, vegetable and grain food and beverage fermentations. However, the numbers, diversity and plant-specific adaptions of LAB found on plant tissues prior to the start of those fermentations are not well understood. When measured, these bacteria have been recovered from the aerial surfaces of plants in a range from <10 CFU g-1 to over 108.5 CFU g-1 of plant tissue and in lower quantities from the soil and rhizosphere. Plant-associated LAB include well-known generalist taxa such as Lactobacillus plantarum and Leuconostoc mesenteroides, which are essential for numerous food and beverage fermentations. Other plant-associated LAB encompass specialist taxa such as Lactobacillus florum and Fructobacillus, many of which were discovered relatively recently and their significance on plants and in foods is not yet recognized. LAB recovered from plants possess the capacity to consume plant sugars, detoxify phenolic compounds and tolerate the numerous biotic and abiotic stresses common to plant surfaces. Although most generalist and some specialist LAB grow rapidly in food and beverages fermentations and can cause spoilage of fresh and fermented fruits and vegetables, the importance of living plants as habitats for these bacteria and LAB contributions to plant microbiomes remain to be shown.
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Affiliation(s)
- Annabelle O Yu
- Department of Food Science & Technology, University of California Davis, Davis, CA, USA
| | - Johan H J Leveau
- Department of Plant Pathology, University of California Davis, Davis, CA, USA
| | - Maria L Marco
- Department of Food Science & Technology, University of California Davis, Davis, CA, USA
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15
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Cai YX, Wang JH, McAuley C, Augustin MA, Terefe NS. Fermentation for enhancing the bioconversion of glucoraphanin into sulforaphane and improve the functional attributes of broccoli puree. J Funct Foods 2019. [DOI: 10.1016/j.jff.2019.103461] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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16
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Kim J, Choi KB, Park JH, Kim KH. Metabolite profile changes and increased antioxidative and antiinflammatory activities of mixed vegetables after fermentation by Lactobacillus plantarum. PLoS One 2019; 14:e0217180. [PMID: 31116776 PMCID: PMC6530839 DOI: 10.1371/journal.pone.0217180] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/06/2019] [Indexed: 02/05/2023] Open
Abstract
Fermented vegetables have emerged as prebiotics with various health benefits. However, the possible mechanisms behind their health benefits are unclear. To relate the metabolite profile changes in fermented mixed vegetables with associated health benefits of fermented vegetables, we analyzed the metabolite profiles of mixed vegetables, before and after fermentation by Lactobacillus plantarum, using gas chromatography/time-of-flight-mass spectrometry (GC/TOF-MS). To analyze health benefits of fermented vegetables, antioxidative and antiinflammatory activities were measured using RAW 264.7 cells. Among 78 metabolites identified by GC/TOF-MS in this study, those significantly increased after fermentation include antioxidative and/or antiinflammatory agents such as lactate, 3-phennyllactate, indole-3-lactate, β-hydroxybutyrate, γ-aminobutyrate, and glycerol. These metabolites may have been either newly synthesized or depolymerized from high molecular weight polymers from vegetables during fermentation. This is the first metabolomics study to relate metabolite profile changes with increased health benefits of fermented vegetables.
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Affiliation(s)
- Jungyeon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, South Korea
| | - Kum-Boo Choi
- Pulmuone Institute of Technology, Pulmuone, Seoul, South Korea
| | - Ju Hun Park
- Pulmuone Institute of Technology, Pulmuone, Seoul, South Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, South Korea
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17
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Choi J, Kim YK, Han PL. Extracellular Vesicles Derived from Lactobacillus plantarum Increase BDNF Expression in Cultured Hippocampal Neurons and Produce Antidepressant-like Effects in Mice. Exp Neurobiol 2019; 28:158-171. [PMID: 31138987 PMCID: PMC6526105 DOI: 10.5607/en.2019.28.2.158] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 03/25/2019] [Accepted: 03/28/2019] [Indexed: 12/26/2022] Open
Abstract
Gut microbiota play a role in regulating mental disorders, but the mechanism by which gut microbiota regulate brain function remains unclear. Gram negative and positive gut bacteria release membrane-derived extracellular vesicles (EVs), which function in microbiota-host intercellular communication. In the present study, we investigated whether Lactobacillus plantarum derived EVs (L-EVs) could have a role in regulating neuronal function and stress-induced depressive-like behaviors. HT22 cells treated with the stress hormone glucocorticoid (GC; corticosterone) had reduced expression of Bdnf and Sirt1, whereas L-EV treatment reversed GC-induced decreased expression of Bdnf and Sirt1. The siRNA-mediated knockdown of Sirt1 in HT22 cells decreased Bdnf4, a splicing variant of Bdnf, and Creb expression, suggesting that Sirt1 plays a role in L-EV-induced increase of BDNF and CREB expression. Mice exposed to restraint for 2-h daily for 14 days (CRST) exhibited depressive-like behaviors, and these CRST-treated mice had reduced expression of Bdnf and Nt4/5 in the hippocampus. In contrast, L-EV injection prior to each restraint treatment blocked the reduced expression of Bdnf and Nt4/5, and stress-induced depressive-like behaviors. Furthermore, L-EV treatment in CRST-treated mice also rescued the reduced expression of Bdnf, and blocked stress-induced depressive-like behaviors. These results suggest that Lactobacillus derived EVs can change the expression of neurotropic factors in the hippocampus and afford antidepressant-like effects in mice with stress-induced depression.
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Affiliation(s)
- Juli Choi
- Department of Brain and Cognitive Sciences, Ewha Womans University, Seoul 03760, Korea
| | | | - Pyung-Lim Han
- Department of Brain and Cognitive Sciences, Ewha Womans University, Seoul 03760, Korea.,Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
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18
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van Mastrigt O, Egas RA, Lillevang SK, Abee T, Smid EJ. Application of a partial cell recycling chemostat for continuous production of aroma compounds at near-zero growth rates. BMC Res Notes 2019; 12:173. [PMID: 30909948 PMCID: PMC6434626 DOI: 10.1186/s13104-019-4213-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/18/2019] [Indexed: 12/22/2022] Open
Abstract
Objective The partial cell recycling chemostat is a modification of the chemostat in which cells are partially recycled towards the bioreactor. This allows using dilution rates higher than the maximum growth rate resulting in higher biomass concentrations and increased process rates. In this study, we demonstrate with a single observation that this system can also be used to study microorganisms at near-zero growth rates and as production system for compounds specific for slow growth, such as those typical for ripened cheese. Results Lactococcus lactis FM03-V2 was cultivated at growth rates between 0.0025 and 0.025 h−1. Detailed analysis of produced aroma compounds revealed that levels of particular compounds were clearly affected by the growth rate within the studied range demonstrating that we can steer the aroma production by controlling the growth rate. With this approach, we also experimentally validated that the maintenance coefficient of this dairy strain decreased at near-zero growth rates (6.4-fold). An exponentially decreasing maintenance coefficient was included in the growth model, enabling accurate prediction of biomass accumulation in the partial cell recycling chemostat. This study demonstrates the potential of partial cell recycling chemostat both as aroma production system at near-zero growth rates and as unique research tool. Electronic supplementary material The online version of this article (10.1186/s13104-019-4213-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oscar van Mastrigt
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Reinier A Egas
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Tjakko Abee
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Eddy J Smid
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
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19
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Hausmann B, Pelikan C, Rattei T, Loy A, Pester M. Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member. mBio 2019; 10:e02189-18. [PMID: 30755506 PMCID: PMC6372793 DOI: 10.1128/mbio.02189-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/04/2019] [Indexed: 01/05/2023] Open
Abstract
Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterize "Candidatus Desulfosporosinus infrequens," a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling. We obtained its near-complete genome by metagenomics of acidic peat soil. In addition, we analyzed anoxic peat soil incubated under in situ-like conditions for 50 days by Desulfosporosinus-targeted qPCR and metatranscriptomics. The Desulfosporosinus population stayed at a constant low abundance under all incubation conditions, averaging 1.2 × 106 16S rRNA gene copies per cm³ soil. In contrast, transcriptional activity of "Ca. Desulfosporosinus infrequens" increased at day 36 by 56- to 188-fold when minor amendments of acetate, propionate, lactate, or butyrate were provided with sulfate, compared to the no-substrate-control. Overall transcriptional activity was driven by expression of genes encoding ribosomal proteins, energy metabolism, and stress response but not by expression of genes encoding cell growth-associated processes. Since our results did not support growth of these highly active microorganisms in terms of biomass increase or cell division, they had to invest their sole energy for maintenance, most likely counterbalancing acidic pH conditions. This finding explains how a rare biosphere member can contribute to a biogeochemically relevant process while remaining in a zero-growth state over a period of 50 days.IMPORTANCE The microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat's biomass. Dormancy or starvation is typically used to explain the persistence of low-abundance microorganisms in the environment. We show that a low-abundance microorganism can be highly transcriptionally active while remaining in a zero-growth state for at least 7 weeks. Our results provide evidence that this zero growth at a high cellular activity state is driven by maintenance requirements. We show that this is true for a microbial keystone species, in particular a cosmopolitan but permanently low-abundance sulfate-reducing microorganism in wetlands that is involved in counterbalancing greenhouse gas emissions. In summary, our results provide an important step forward in understanding time-resolved activities of rare biosphere members relevant for ecosystem functions.
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Affiliation(s)
- Bela Hausmann
- Research Network Chemistry meets Microbiology, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Claus Pelikan
- Research Network Chemistry meets Microbiology, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Research Network Chemistry meets Microbiology, Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Research Network Chemistry meets Microbiology, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Michael Pester
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Microorganisms, Leibniz Institute DSMZ, Braunschweig, Germany
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
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20
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Mendonça AA, da Silva PKN, Calazans TLS, de Souza RB, de Barros Pita W, Elsztein C, de Morais Junior MA. Lactobacillus vini: mechanistic response to stress by medium acidification. Microbiology (Reading) 2019; 165:26-36. [DOI: 10.1099/mic.0.000738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | | | | | | | - Will de Barros Pita
- 3Department of Antibiotics, Federal University of Pernambuco, Recife, Brazil
| | - Carolina Elsztein
- 1Department of Genetics, Federal University of Pernambuco, Recife, Brazil
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21
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Quantitative physiology and aroma formation of a dairy Lactococcus lactis at near-zero growth rates. Food Microbiol 2018. [DOI: 10.1016/j.fm.2018.01.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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22
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Zhang D, Strawn M, Novak JT, Wang ZW. Kinetic modeling of the effect of solids retention time on methanethiol dynamics in anaerobic digestion. WATER RESEARCH 2018; 138:301-311. [PMID: 29614458 DOI: 10.1016/j.watres.2018.03.035] [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: 11/14/2017] [Revised: 03/11/2018] [Accepted: 03/13/2018] [Indexed: 06/08/2023]
Abstract
The highly volatile methanethiol (MT) with an extremely low odor threshold and distinctive putrid smell is often identified as a major odorous compound generated under anaerobic conditions. As an intermediate compound in the course of anaerobic digestion, the extent of MT emission is closely related to the time of anaerobic reaction. In this study, lab-scale anaerobic digesters were operated at solids retention time (SRTs) of 15, 20, 25, 30, 40 and 50 days to investigate the effect of SRT on MT emission. The experimental results demonstrated a bell-shaped curve of MT emission versus SRT with a peak around 20 days SRT. In order to understand this SRT effect, a kinetic model was developed to describe MT production and utilization dynamics in the course of anaerobic digestion and calibrated with the experimental results collected from this study. The model outcome revealed that the high protein content in the feed sludge together with the large maintenance coefficient of MT fermenters are responsible for the peak MT emission emergence in the range of typical SRT used for anaerobic digestion. A further analysis of the kinetic model shows that it can be extensively simplified with reasonable approximation to a form that anaerobic digestion practitioners could easily use to predict the MT and SRT relationship.
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Affiliation(s)
- Dian Zhang
- Occoquan Laboratory, Department of Civil and Environmental Engineering, Virginia Tech, 9408 Prince William Street, Manassas, VA 20110, USA
| | - Mary Strawn
- Arlington County Water Pollution Control Bureau, 3402 S Glebe Rd, Arlington, VA 22202, USA
| | - John T Novak
- Occoquan Laboratory, Department of Civil and Environmental Engineering, Virginia Tech, 9408 Prince William Street, Manassas, VA 20110, USA
| | - Zhi-Wu Wang
- Occoquan Laboratory, Department of Civil and Environmental Engineering, Virginia Tech, 9408 Prince William Street, Manassas, VA 20110, USA.
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23
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Bacterial Adaptation to the Host's Diet Is a Key Evolutionary Force Shaping Drosophila-Lactobacillus Symbiosis. Cell Host Microbe 2018; 24:109-119.e6. [PMID: 30008290 PMCID: PMC6054917 DOI: 10.1016/j.chom.2018.06.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 04/27/2018] [Accepted: 05/11/2018] [Indexed: 01/09/2023]
Abstract
Animal-microbe facultative symbioses play a fundamental role in ecosystem and organismal health. Yet, due to the flexible nature of their association, the selection pressures that act on animals and their facultative symbionts remain elusive. Here we apply experimental evolution to Drosophila melanogaster associated with its growth-promoting symbiont Lactobacillus plantarum, representing a well-established model of facultative symbiosis. We find that the diet of the host, rather than the host itself, is a predominant driving force in the evolution of this symbiosis. Furthermore, we identify a mechanism resulting from the bacterium's adaptation to the diet, which confers growth benefits to the colonized host. Our study reveals that bacterial adaptation to the host's diet may be the foremost step in determining the evolutionary course of a facultative animal-microbe symbiosis. L. plantarum experimental evolution leads to the improvement of its symbiotic benefit L. plantarum increases its growth-promotion ability by adapting to Drosophila diet Mutation of ackA gene enhances both L. plantarum fitness and benefit to the host N-acetyl-glutamine production is sufficient to improve L. plantarum growth promotion
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24
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Constraint-based modeling in microbial food biotechnology. Biochem Soc Trans 2018; 46:249-260. [PMID: 29588387 PMCID: PMC5906707 DOI: 10.1042/bst20170268] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 12/19/2022]
Abstract
Genome-scale metabolic network reconstruction offers a means to leverage the value of the exponentially growing genomics data and integrate it with other biological knowledge in a structured format. Constraint-based modeling (CBM) enables both the qualitative and quantitative analyses of the reconstructed networks. The rapid advancements in these areas can benefit both the industrial production of microbial food cultures and their application in food processing. CBM provides several avenues for improving our mechanistic understanding of physiology and genotype–phenotype relationships. This is essential for the rational improvement of industrial strains, which can further be facilitated through various model-guided strain design approaches. CBM of microbial communities offers a valuable tool for the rational design of defined food cultures, where it can catalyze hypothesis generation and provide unintuitive rationales for the development of enhanced community phenotypes and, consequently, novel or improved food products. In the industrial-scale production of microorganisms for food cultures, CBM may enable a knowledge-driven bioprocess optimization by rationally identifying strategies for growth and stability improvement. Through these applications, we believe that CBM can become a powerful tool for guiding the areas of strain development, culture development and process optimization in the production of food cultures. Nevertheless, in order to make the correct choice of the modeling framework for a particular application and to interpret model predictions in a biologically meaningful manner, one should be aware of the current limitations of CBM.
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25
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He Q, Cao C, Hui W, Yu J, Zhang H, Zhang W. Genomic resequencing combined with quantitative proteomic analyses elucidate the survival mechanisms of Lactobacillus plantarum P-8 in a long-term glucose-limited experiment. J Proteomics 2018; 176:37-45. [PMID: 29414317 DOI: 10.1016/j.jprot.2018.01.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/09/2018] [Accepted: 01/19/2018] [Indexed: 12/20/2022]
Abstract
Lactobacillus plantarum, commonly isolated from plant material, is widely used to produce various types of fermented foods. However, nutrient-limiting conditions are often encountered during industrial applications. The present study aimed to investigate the response of L. plantarum P-8 to glucose-limited conditions in a long-term experiment. Genotypic and proteomic changes in L. plantarum P-8 were monitored over 3 years in glucose-limited and glucose-normal media using whole-genome resequencing and tandem mass tag-based quantitative proteomic analysis. Results showed that L. plantarum employed numerous survival mechanisms, including alteration of the cell envelope, activation of the PTS system, accumulation and consumption of amino acids, increase in the metabolism of carbohydrates (via glycolysis, citric acid cycle, and pyruvate metabolism), and increase in the production of ATP in response to glucose starvation. This study demonstrates the feasibility of experimental evolution of L. plantarum P-8, while whole-genome resequencing of adapted isolates provided clues toward bacterial functions involved and a deeper mechanistic understanding of the adaptive response of L. plantarum to glucose-limited conditions. SIGNIFICANCE We have conducted a 3-year experiment monitoring genotypic and proteomic changes in Lactobacillus plantarum P-8 in glucose-limited and glucose-normal media. Whole-genome resequencing and tandem mass tag-based quantitative proteomics were performed for analyzing genomic evolution of L. plantarum P-8 in glucose-limited and glucose-normal conditions. In addition, differential expressed proteins in all generations between these two conditions were identified and functions of these proteins specific to L group were predicted. L. plantarum employed numerous survival mechanisms, including alteration of the cell envelope, activation of the PTS system, accumulation and consumption of amino acids, increase in the metabolism of carbohydrates (glycolysis, citric acid cycle, and pyruvate metabolism), and increase in the production of ATP in response to glucose starvation.
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Affiliation(s)
- Qiuwen He
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Chenxia Cao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Wenyan Hui
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China.
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26
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Abstract
Lactic acid bacteria (LAB) ferment plants, fish, meats and milk and turn them into tasty food products with increased shelf life; other LAB help digesting food and create a healthy environment in the intestine. The economic and societal importance of these relatively simple and small bacteria is immense. In this review we hope to show that their adaptations to nutrient-rich environments provides fascinating and often puzzling behaviours that give rise to many fundamental evolutionary biological questions in need of a systems biology approach. We will provide examples of such questions, compare the (metabolic) behaviour of LAB to that of other model organisms, and provide the latest insights, if available.
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Affiliation(s)
- Bas Teusink
- Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, O
- 2 Building, Section Systems Bioinformatics, Location Code 2E51, De Boelelaan 1085, NL-1081HV Amsterdam, The Netherlands.,Top Institute Food and Nutrition, 6700 AN Wageningen, The Netherlands
| | - Douwe Molenaar
- Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, O
- 2 Building, Section Systems Bioinformatics, Location Code 2E51, De Boelelaan 1085, NL-1081HV Amsterdam, The Netherlands.,Top Institute Food and Nutrition, 6700 AN Wageningen, The Netherlands
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27
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Branco Dos Santos F, Olivier BG, Boele J, Smessaert V, De Rop P, Krumpochova P, Klau GW, Giera M, Dehottay P, Teusink B, Goffin P. Probing the Genome-Scale Metabolic Landscape of Bordetella pertussis, the Causative Agent of Whooping Cough. Appl Environ Microbiol 2017; 83:e01528-17. [PMID: 28842544 PMCID: PMC5648915 DOI: 10.1128/aem.01528-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 08/23/2017] [Indexed: 11/20/2022] Open
Abstract
Whooping cough is a highly contagious respiratory disease caused by Bordetella pertussis Despite widespread vaccination, its incidence has been rising alarmingly, and yet, the physiology of B. pertussis remains poorly understood. We combined genome-scale metabolic reconstruction, a novel optimization algorithm, and experimental data to probe the full metabolic potential of this pathogen, using B. pertussis strain Tohama I as a reference. Experimental validation showed that B. pertussis secretes a significant proportion of nitrogen as arginine and purine nucleosides, which may contribute to modulation of the host response. We also found that B. pertussis can be unexpectedly versatile, being able to metabolize many compounds while displaying minimal nutrient requirements. It can grow without cysteine, using inorganic sulfur sources, such as thiosulfate, and it can grow on organic acids, such as citrate or lactate, as sole carbon sources, providing in vivo demonstration that its tricarboxylic acid (TCA) cycle is functional. Although the metabolic reconstruction of eight additional strains indicates that the structural genes underlying this metabolic flexibility are widespread, experimental validation suggests a role of strain-specific regulatory mechanisms in shaping metabolic capabilities. Among five alternative strains tested, three strains were shown to grow on substrate combinations requiring a functional TCA cycle, but only one strain could use thiosulfate. Finally, the metabolic model was used to rationally design growth media with >2-fold improvements in pertussis toxin production. This study thus provides novel insights into B. pertussis physiology and highlights the potential, but also the limitations, of models based solely on metabolic gene content.IMPORTANCE The metabolic capabilities of Bordetella pertussis, the causative agent of whooping cough, were investigated from a systems-level perspective. We constructed a comprehensive genome-scale metabolic model for B. pertussis and challenged its predictions experimentally. This systems approach shed light on new potential host-microbe interactions and allowed us to rationally design novel growth media with >2-fold improvements in pertussis toxin production. Most importantly, we also uncovered the potential for metabolic flexibility of B. pertussis (significantly larger range of substrates than previously alleged; novel active pathways allowing growth in minimal, nearly mineral nutrient combinations where only the carbon source must be organic), although our results also highlight the importance of strain-specific regulatory determinants in shaping metabolic capabilities. Deciphering the underlying regulatory mechanisms appears to be crucial for a comprehensive understanding of B. pertussis's lifestyle and the epidemiology of whooping cough. The contribution of metabolic models in this context will require the extension of the genome-scale metabolic model to integrate this regulatory dimension.
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Affiliation(s)
- Filipe Branco Dos Santos
- Systems Bioinformatics/AIMMS, Vrije University Amsterdam, Amsterdam, The Netherlands
- Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Brett G Olivier
- Systems Bioinformatics/AIMMS, Vrije University Amsterdam, Amsterdam, The Netherlands
- Centrum Wiskunde & Informatica (CWI), Amsterdam, The Netherlands
| | - Joost Boele
- Systems Bioinformatics/AIMMS, Vrije University Amsterdam, Amsterdam, The Netherlands
| | | | | | - Petra Krumpochova
- Systems Bioinformatics/AIMMS, Vrije University Amsterdam, Amsterdam, The Netherlands
| | - Gunnar W Klau
- Centrum Wiskunde & Informatica (CWI), Amsterdam, The Netherlands
- Algorithmic Bioinformatics, Heinrich Heine University, Düsseldorf, Germany
| | - Martin Giera
- Systems Bioinformatics/AIMMS, Vrije University Amsterdam, Amsterdam, The Netherlands
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Bas Teusink
- Systems Bioinformatics/AIMMS, Vrije University Amsterdam, Amsterdam, The Netherlands
| | - Philippe Goffin
- GSK Vaccines, Rixensart, Belgium
- Laboratoire de Génétique et Physiologie Bactérienne, IBMM, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
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Desguin B, Soumillion P, Hausinger RP, Hols P. Unexpected complexity in the lactate racemization system of lactic acid bacteria. FEMS Microbiol Rev 2017; 41:S71-S83. [DOI: 10.1093/femsre/fux021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/11/2017] [Indexed: 12/30/2022] Open
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van Niel EWJ, Bergdahl B, Hahn-Hägerdal B. Close to the Edge: Growth Restrained by the NAD(P)H/ATP Formation Flux Ratio. Front Microbiol 2017; 8:1149. [PMID: 28690597 PMCID: PMC5479917 DOI: 10.3389/fmicb.2017.01149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/07/2017] [Indexed: 11/13/2022] Open
Abstract
Most fermentative microorganisms grow well-under anaerobic conditions managing a balanced redox and appropriate energy metabolism, but a few species do exist in which cells have to cope with inadequate energy recovery or capture and/or redox balancing. Two cases of these species, i.e., the metabolically engineered Saccharomyces cerevisiae enabling it to ferment xylose and Lactobacillus reuteri fermenting glucose via the phosphoketolase pathway, are here used to introduce a quantification parameter to capture what limits the growth rate of these microorganisms under anaerobic conditions. This dimensionless parameter, the cofactor formation flux ratio (RJ), is the ratio between the redox formation flux (JNADH+NADPH), and the energy carrier formation flux (JATP), which are mainly connected to the central carbon pathways. Data from metabolic flux analyses performed in previous and present studies were used to estimate the RJ-values. Even though both microorganisms possess different central pathways, a similar relationship between RJ and the specific growth rate (μ) was found. Furthermore, for both microorganisms external electron acceptors moderately reduced the RJ-value, thereby raising the μ accordingly. Based on the emerging profile of this relationship an interpretation is presented suggesting that this quantitative analysis can be applied beyond the two microbial species experimentally investigated in the current study to provide data for future targeted strain development strategies.
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Affiliation(s)
- Ed W J van Niel
- Division of Applied Microbiology, Lund UniversityLund, Sweden
| | - Basti Bergdahl
- Division of Applied Microbiology, Lund UniversityLund, Sweden
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Du W, Jongbloets JA, Pineda Hernández H, Bruggeman FJ, Hellingwerf KJ, Branco dos Santos F. Photonfluxostat: A method for light-limited batch cultivation of cyanobacteria at different, yet constant, growth rates. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.10.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Abstract
Lactic acid bacteria (LAB) are important starter, commensal, or pathogenic microorganisms. The stress physiology of LAB has been studied in depth for over 2 decades, fueled mostly by the technological implications of LAB robustness in the food industry. Survival of probiotic LAB in the host and the potential relatedness of LAB virulence to their stress resilience have intensified interest in the field. Thus, a wealth of information concerning stress responses exists today for strains as diverse as starter (e.g., Lactococcus lactis), probiotic (e.g., several Lactobacillus spp.), and pathogenic (e.g., Enterococcus and Streptococcus spp.) LAB. Here we present the state of the art for LAB stress behavior. We describe the multitude of stresses that LAB are confronted with, and we present the experimental context used to study the stress responses of LAB, focusing on adaptation, habituation, and cross-protection as well as on self-induced multistress resistance in stationary phase, biofilms, and dormancy. We also consider stress responses at the population and single-cell levels. Subsequently, we concentrate on the stress defense mechanisms that have been reported to date, grouping them according to their direct participation in preserving cell energy, defending macromolecules, and protecting the cell envelope. Stress-induced responses of probiotic LAB and commensal/pathogenic LAB are highlighted separately due to the complexity of the peculiar multistress conditions to which these bacteria are subjected in their hosts. Induction of prophages under environmental stresses is then discussed. Finally, we present systems-based strategies to characterize the "stressome" of LAB and to engineer new food-related and probiotic LAB with improved stress tolerance.
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Gene expression of Lactobacillus plantarum and the commensal microbiota in the ileum of healthy and early SIV-infected rhesus macaques. Sci Rep 2016; 6:24723. [PMID: 27102350 PMCID: PMC4840379 DOI: 10.1038/srep24723] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/04/2016] [Indexed: 12/27/2022] Open
Abstract
Chronic HIV infection results in impairment of gut-associated lymphoid tissue leading to systemic immune activation. We previously showed that in early SIV-infected rhesus macaques intestinal dysfunction is initiated with the induction of the IL-1β pathway in the small intestine and reversed by treatment with an exogenous Lactobacillus plantarum strain. Here, we provide evidence that the transcriptomes of L. plantarum and ileal microbiota are not altered shortly after SIV infection. L. plantarum adapts to the small intestine by expressing genes required for tolerating oxidative stress, modifying cell surface composition, and consumption of host glycans. The ileal microbiota of L. plantarum-containing healthy and SIV+ rhesus macaques also transcribed genes for host glycan metabolism as well as for cobalamin biosynthesis. Expression of these pathways by bacteria were proposed but not previously demonstrated in the mammalian small intestine.
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Reverón I, de las Rivas B, Matesanz R, Muñoz R, López de Felipe F. Molecular adaptation of Lactobacillus plantarum WCFS1 to gallic acid revealed by genome-scale transcriptomic signature and physiological analysis. Microb Cell Fact 2015; 14:160. [PMID: 26453568 PMCID: PMC4600210 DOI: 10.1186/s12934-015-0345-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 09/23/2015] [Indexed: 11/10/2022] Open
Abstract
Background Gallic acid (GA) is a model hydroxybenzoic acid that occurs esterified in the lignocellulosic biomass of higher plants. GA displays relevant biological activities including anticancer properties. Owing to its antimicrobial and cellulase-inhibiting activities, GA also imposes constraints to the fermentability of lignocellulosic hydrolysates. In depth-knowledge of the mechanisms used by tolerant microorganisms to adapt to hydroxybenzoic acids would be a step forward to improve the bioavailability of GA or select/engineer production hosts with improved metabolic traits for the bioconversion of pretreated lignocellulosic biomass. Results Whole genome transcriptional profiling using DNA microarrays was used to characterize the molecular response of Lactobacillus plantarum WCFS1 to GA. Expression levels of 14 and 40 genes were differentially regulated at 1.5 and 15 mM GA, respectively. The transcriptomic analysis identified a marked induction of genes with confirmed or related roles to gastrointestinal survival, the repression of genes coding for certain ABC-type transporters and modulation of genes involved in the control of intracellular ammonia levels, among other responses. Most notably, a core set of genes dedicated to produce GA from polyphenols (tanBLp), decarboxylate GA to pyrogallol (lpdB, lpdC and lpdD) and transport functions (lp_2943) was highly overexpressed at both GA concentrations. Correspondingly, resting cells of strain WCFS1 induced by GA, but not their non-induced controls, produced pyrogallol. Gene expression and organization of genes involved in GA metabolism suggested a chemiosmotic mechanism of energy generation. Resting cells of L. plantarum induced by GA generated a membrane potential and a pH gradient across the membrane immediately upon addition of GA. Altogether, transcriptome profiling correlated with physiological observations indicating that a proton motive force could be generated during GA metabolism as a result of electrogenic GA uptake coupled with proton consumption by the intracellular gallate decarboxylase. Conclusions The combination of transcriptome and physiological analyses revealed versatile molecular mechanisms involved in the adaptation of L. plantarum to GA. These data provide a platform to improve the survival of Lactobacillus in the gut. Our data may also guide the selection/engineering of microorganisms that better tolerate phenolic inhibitors present in pretreated lignocellulosic feedstocks. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0345-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Inés Reverón
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain.
| | - Blanca de las Rivas
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain.
| | - Ruth Matesanz
- Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain.
| | - Rosario Muñoz
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain.
| | - Félix López de Felipe
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain.
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Physiological and Transcriptional Responses of Different Industrial Microbes at Near-Zero Specific Growth Rates. Appl Environ Microbiol 2015; 81:5662-70. [PMID: 26048933 DOI: 10.1128/aem.00944-15] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The current knowledge of the physiology and gene expression of industrially relevant microorganisms is largely based on laboratory studies under conditions of rapid growth and high metabolic activity. However, in natural ecosystems and industrial processes, microbes frequently encounter severe calorie restriction. As a consequence, microbial growth rates in such settings can be extremely slow and even approach zero. Furthermore, uncoupling microbial growth from product formation, while cellular integrity and activity are maintained, offers perspectives that are economically highly interesting. Retentostat cultures have been employed to investigate microbial physiology at (near-)zero growth rates. This minireview compares information from recent physiological and gene expression studies on retentostat cultures of the industrially relevant microorganisms Lactobacillus plantarum, Lactococcus lactis, Bacillus subtilis, Saccharomyces cerevisiae, and Aspergillus niger. Shared responses of these organisms to (near-)zero growth rates include increased stress tolerance and a downregulation of genes involved in protein synthesis. Other adaptations, such as changes in morphology and (secondary) metabolite production, were species specific. This comparison underlines the industrial and scientific significance of further research on microbial (near-)zero growth physiology.
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Genome-wide transcriptional responses to carbon starvation in nongrowing Lactococcus lactis. Appl Environ Microbiol 2015; 81:2554-61. [PMID: 25636846 DOI: 10.1128/aem.03748-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This paper describes the transcriptional adaptations of nongrowing, retentostat cultures of Lactococcus lactis to starvation. Near-zero-growth cultures (μ = 0.0001 h(-1)) obtained by extended retentostat cultivation were exposed to starvation by termination of the medium supply for 24 h, followed by a recovery period of another 24 h by reinitiating the medium supply to the retentostat culture. During starvation, the viability of the culture was largely retained, and the expression of genes involved in transcription and translational machineries, cell division, and cell membrane energy metabolism was strongly repressed. Expression of these genes was largely recovered following the reinitiation of the medium supply. Starvation triggered the elevated expression of genes associated with synthesis of branched-chain amino acids, histidine, purine, and riboflavin. The expression of these biosynthesis genes was found to remain at an elevated level after reinitiation of the medium supply. In addition, starvation induced the complete gene set predicted to be involved in natural competence in L. lactis KF147, and the elevated expression of these genes was sustained during the subsequent recovery period, but our attempts to experimentally demonstrate natural transformation in these cells failed. Mining the starvation response gene set identified a conserved cis-acting element that resembles the lactococcal CodY motif in the upstream regions of genes associated with transcription and translational machineries, purine biosynthesis, and natural transformation in L. lactis, suggesting a role for CodY in the observed transcriptome adaptations to starvation in nongrowing cells.
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Overkamp W, Ercan O, Herber M, van Maris AJA, Kleerebezem M, Kuipers OP. Physiological and cell morphology adaptation of Bacillus subtilis at near-zero specific growth rates: a transcriptome analysis. Environ Microbiol 2014; 17:346-63. [PMID: 25367190 DOI: 10.1111/1462-2920.12676] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 10/10/2014] [Accepted: 10/16/2014] [Indexed: 11/27/2022]
Abstract
Nutrient scarcity is a common condition in nature, but the resulting extremely low growth rates (below 0.025 h(-1) ) are an unexplored research area in Bacillus subtilis. To understand microbial life in natural environments, studying the adaptation of B. subtilis to near-zero growth conditions is relevant. To this end, a chemostat modified for culturing an asporogenous B. subtilis sigF mutant strain at extremely low growth rates (also named a retentostat) was set up, and biomass accumulation, culture viability, metabolite production and cell morphology were analysed. During retentostat culturing, the specific growth rate decreased to a minimum of 0.00006 h(-1) , corresponding to a doubling time of 470 days. The energy distribution between growth and maintenance-related processes showed that a state of near-zero growth was reached. Remarkably, a filamentous cell morphology emerged, suggesting that cell separation is impaired under near-zero growth conditions. To evaluate the corresponding molecular adaptations to extremely low specific growth, transcriptome changes were analysed. These revealed that cellular responses to near-zero growth conditions share several similarities with those of cells during the stationary phase of batch growth. However, fundamental differences between these two non-growing states are apparent by their high viability and absence of stationary phase mutagenesis under near-zero growth conditions.
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Affiliation(s)
- Wout Overkamp
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands; Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA, Delft, The Netherlands
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Enantioselective regulation of lactate racemization by LarR in Lactobacillus plantarum. J Bacteriol 2014; 197:219-30. [PMID: 25349156 DOI: 10.1128/jb.02192-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Lactobacillus plantarum is a lactic acid bacterium that produces a racemic mixture of l- and d-lactate from sugar fermentation. The interconversion of lactate isomers is performed by a lactate racemase (Lar) that is transcriptionally controlled by the l-/d-lactate ratio and maximally induced in the presence of l-lactate. We previously reported that the Lar activity depends on the expression of two divergently oriented operons: (i) the larABCDE operon encodes the nickel-dependent lactate racemase (LarA), its maturases (LarBCE), and a lactic acid channel (LarD), and (ii) the larR(MN)QO operon encodes a transcriptional regulator (LarR) and a four-component ABC-type nickel transporter [Lar(MN), in which the M and N components are fused, LarQ, and LarO]. LarR is a novel regulator of the Crp-Fnr family (PrfA group). Here, the role of LarR was further characterized in vivo and in vitro. We show that LarR is a positive regulator that is absolutely required for the expression of Lar activity. Using gel retardation experiments, we demonstrate that LarR binds to a 16-bp palindromic sequence (Lar box motif) that is present in the larR-larA intergenic region. Mutations in the Lar box strongly affect LarR binding and completely abolish transcription from the larA promoter (PlarA). Two half-Lar boxes located between the Lar box and the -35 box of PlarA promote LarR multimerization on DNA, and point mutations within one or both half-Lar boxes inhibit PlarA induction by l-lactate. Gel retardation and footprinting experiments indicate that l-lactate has a positive effect on the binding and multimerization of LarR, while d-lactate antagonizes the positive effect of l-lactate. A possible mechanism of LarR regulation by lactate enantiomers is proposed.
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Molecular and metabolic adaptations of Lactococcus lactis at near-zero growth rates. Appl Environ Microbiol 2014; 81:320-31. [PMID: 25344239 DOI: 10.1128/aem.02484-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This paper describes the molecular and metabolic adaptations of Lactococcus lactis during the transition from a growing to a near-zero growth state by using carbon-limited retentostat cultivation. Transcriptomic analyses revealed that metabolic patterns shifted between lactic- and mixed-acid fermentations during retentostat cultivation, which appeared to be controlled at the level of transcription of the corresponding pyruvate dissipation-encoding genes. During retentostat cultivation, cells continued to consume several amino acids but also produced specific amino acids, which may derive from the conversion of glycolytic intermediates. We identify a novel motif containing CTGTCAG in the upstream regions of several genes related to amino acid conversion, which we propose to be the target site for CodY in L. lactis KF147. Finally, under extremely low carbon availability, carbon catabolite repression was progressively relieved and alternative catabolic functions were found to be highly expressed, which was confirmed by enhanced initial acidification rates on various sugars in cells obtained from near-zero-growth cultures. The present integrated transcriptome and metabolite (amino acids and previously reported fermentation end products) study provides molecular understanding of the adaptation of L. lactis to conditions supporting low growth rates and expands our earlier analysis of the quantitative physiology of this bacterium at near-zero growth rates toward gene regulation patterns involved in zero-growth adaptation.
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Panikov NS, Mandalakis M, Dai S, Mulcahy LR, Fowle W, Garrett WS, Karger BL. Near-zero growth kinetics of Pseudomonas putida deduced from proteomic analysis. Environ Microbiol 2014; 17:215-28. [PMID: 25088710 DOI: 10.1111/1462-2920.12584] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/25/2014] [Indexed: 11/26/2022]
Abstract
Intensive microbial growth typically observed in laboratory rarely occurs in nature. Because of severe nutrient deficiency, natural populations exhibit near-zero growth (NZG). There is a long-standing controversy about sustained NZG, specifically whether there is a minimum growth rate below which cells die or whether cells enter a non-growing maintenance state. Using chemostat with cell retention (CCR) of Pseudomonas putida, we resolve this controversy and show that under NZG conditions, bacteria differentiate into growing and VBNC (viable but not non-culturable) forms, the latter preserving measurable catabolic activity. The proliferating cells attained a steady state, their slow growth balanced by VBNC production. Proteomic analysis revealed upregulated (transporters, stress response, self-degrading enzymes and extracellular polymers) and downregulated (ribosomal, chemotactic and primary biosynthetic enzymes) proteins in the CCR versus batch culture. Based on these profiles, we identified intracellular processes associated with NZG and generated a mathematical model that simulated the observations. We conclude that NZG requires controlled partial self-digestion and deep reconfiguration of the metabolic machinery that results in the biosynthesis of new products and development of broad stress resistance. CCR allows efficient on-line control of NZG including VBNC production. A well-nuanced understanding of NZG is important to understand microbial processes in situ and for optimal design of environmental technologies.
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Affiliation(s)
- Nicolai S Panikov
- Department of Biology, Northeastern University, Boston, MA, 02115, USA; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, 02115, USA
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Marozava S, Röling WF, Seifert J, Küffner R, von Bergen M, Meckenstock RU. Physiology of Geobacter metallireducens under excess and limitation of electron donors. Part II. Mimicking environmental conditions during cultivation in retentostats. Syst Appl Microbiol 2014; 37:287-95. [DOI: 10.1016/j.syapm.2014.02.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 02/25/2014] [Accepted: 02/28/2014] [Indexed: 11/15/2022]
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Metabolic responses of Lactobacillus plantarum strains during fermentation and storage of vegetable and fruit juices. Appl Environ Microbiol 2014; 80:2206-15. [PMID: 24487533 DOI: 10.1128/aem.03885-13] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Strains of Lactobacillus plantarum were grown and stored in cherry (ChJ), pineapple (PJ), carrot (CJ), and tomato (TJ) juices to mimic the chemical composition of the respective matrices. Wheat flour hydrolysate (WFH), whey milk (W), and MRS broth were also used as representatives of other ecosystems. The growth rates and cell densities of L. plantarum strains during fermentation (24 h at 30°C) and storage (21 days at 4°C) differed only in part, being mainly influenced by the matrix. ChJ and PJ were the most stressful juices for growth and survival. Overall, the growth in juices was negatively correlated with the initial concentration of malic acid and carbohydrates. The consumption of malic acid was noticeable for all juices, but mainly during fermentation and storage of ChJ. Decreases of branched-chain amino acids (BCAA)-with the concomitant increase of their respective branched alcohols-and His and increases of Glu and gamma-aminobutyric acid (GABA) were the main traits of the catabolism of free amino acids (FAA), which were mainly evident under less acidic conditions (CJ and TJ). The increase of Tyr was found only during storage of ChJ. Some aldehydes (e.g., 3-methyl-butanal) were reduced to the corresponding alcohols (e.g., 3-methyl-1-butanol). After both fermentation and storage, acetic acid increased in all fermented juices, which implied the activation of the acetate kinase route. Diacetyl was the ketone found at the highest level, and butyric acid increased in almost all fermented juices. Data were processed through multidimensional statistical analyses. Except for CJ, the juices (mainly ChJ) seemed to induce specific metabolic traits, which differed in part among the strains. This study provided more in-depth knowledge on the metabolic mechanisms of growth and maintenance of L. plantarum in vegetable and fruit habitats, which also provided helpful information to select the most suitable starters for fermentation of targeted matrices.
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Maarleveld TR, Khandelwal RA, Olivier BG, Teusink B, Bruggeman FJ. Basic concepts and principles of stoichiometric modeling of metabolic networks. Biotechnol J 2013; 8:997-1008. [PMID: 23893965 PMCID: PMC4671265 DOI: 10.1002/biot.201200291] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 05/03/2013] [Accepted: 07/01/2013] [Indexed: 12/16/2022]
Abstract
Metabolic networks supply the energy and building blocks for cell growth and maintenance. Cells continuously rewire their metabolic networks in response to changes in environmental conditions to sustain fitness. Studies of the systemic properties of metabolic networks give insight into metabolic plasticity and robustness, and the ability of organisms to cope with different environments. Constraint-based stoichiometric modeling of metabolic networks has become an indispensable tool for such studies. Herein, we review the basic theoretical underpinnings of constraint-based stoichiometric modeling of metabolic networks. Basic concepts, such as stoichiometry, chemical moiety conservation, flux modes, flux balance analysis, and flux solution spaces, are explained with simple, illustrative examples. We emphasize the mathematical definitions and their network topological interpretations.
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Affiliation(s)
- Timo R Maarleveld
- Life Sciences, Center for Mathematics and Computer Science, Amsterdam, The Netherlands; Systems Bioinformatics, Amsterdam Institute for Molecules Medicines and Systems, VU University Amsterdam, Amsterdam, The Netherlands; BioSolar Cells, Wageningen, The Netherlands
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Filannino P, Azzi L, Cavoski I, Vincentini O, Rizzello CG, Gobbetti M, Di Cagno R. Exploitation of the health-promoting and sensory properties of organic pomegranate (Punica granatum L.) juice through lactic acid fermentation. Int J Food Microbiol 2013; 163:184-92. [DOI: 10.1016/j.ijfoodmicro.2013.03.002] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 12/21/2012] [Accepted: 03/03/2013] [Indexed: 12/24/2022]
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44
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Ercan O, Smid EJ, Kleerebezem M. Quantitative physiology ofLactococcus lactisat extreme low-growth rates. Environ Microbiol 2013; 15:2319-32. [DOI: 10.1111/1462-2920.12104] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 01/24/2013] [Accepted: 01/25/2013] [Indexed: 11/26/2022]
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45
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Hugenholtz J. Traditional biotechnology for new foods and beverages. Curr Opin Biotechnol 2013; 24:155-9. [PMID: 23395405 DOI: 10.1016/j.copbio.2013.01.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 12/27/2012] [Accepted: 01/02/2013] [Indexed: 11/18/2022]
Abstract
The food and beverage industry is re-discovering fermentation as a crucial step in product innovation. Fermentation can provide various benefits such as unique flavor, health and nutrition, texture and safety (shelf life), while maintaining a 100% natural label. In this review several examples are presented on how fermentation is used to replace, modify or improve current, artificially produced, foods and beverages and how also fermentation can be used for completely novel consumer products.
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Affiliation(s)
- Jeroen Hugenholtz
- Swammerdam Institute for Life Sciences, University of Amsterdam and Coca-Cola Corporate Research, Mainburger Strasse 19, 84072 Au/Hallertau, Germany.
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Branco dos Santos F, de Vos WM, Teusink B. Towards metagenome-scale models for industrial applications--the case of Lactic Acid Bacteria. Curr Opin Biotechnol 2012. [PMID: 23200025 DOI: 10.1016/j.copbio.2012.11.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We review the uses and limitations of modelling approaches that are in use in the field of Lactic Acid Bacteria (LAB). We describe recent developments in model construction and computational methods, starting from application of such models to monocultures. However, since most applications in food biotechnology involve complex nutrient environments and mixed cultures, we extend the scope to discuss developments in modelling such complex systems. With metagenomics and meta-functional genomics data becoming available, the developments in genome-scale community models are discussed. We conclude that exploratory tools are available and useful, but truly predictive mechanistic models will remain a major challenge in the field.
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Affiliation(s)
- Filipe Branco dos Santos
- Systems Bioinformatics/NISB, Faculty of Earth and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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Lewis NE, Nagarajan H, Palsson BO. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol 2012; 10:291-305. [PMID: 22367118 DOI: 10.1038/nrmicro2737] [Citation(s) in RCA: 537] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Reconstructed microbial metabolic networks facilitate a mechanistic description of the genotype-phenotype relationship through the deployment of constraint-based reconstruction and analysis (COBRA) methods. As reconstructed networks leverage genomic data for insight and phenotype prediction, the development of COBRA methods has accelerated following the advent of whole-genome sequencing. Here, we describe a phylogeny of COBRA methods that has rapidly evolved from the few early methods, such as flux balance analysis and elementary flux mode analysis, into a repertoire of more than 100 methods. These methods have enabled genome-scale analysis of microbial metabolism for numerous basic and applied uses, including antibiotic discovery, metabolic engineering and modelling of microbial community behaviour.
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Affiliation(s)
- Nathan E Lewis
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, USA
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Teusink B, Bachmann H, Molenaar D. Systems biology of lactic acid bacteria: a critical review. Microb Cell Fact 2011; 10 Suppl 1:S11. [PMID: 21995498 PMCID: PMC3231918 DOI: 10.1186/1475-2859-10-s1-s11] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Understanding the properties of a system as emerging from the interaction of well described parts is the most important goal of Systems Biology. Although in the practice of Lactic Acid Bacteria (LAB) physiology we most often think of the parts as the proteins and metabolites, a wider interpretation of what a part is can be useful. For example, different strains or species can be the parts of a community, or we could study only the chemical reactions as the parts of metabolism (and forgetting about the enzymes that catalyze them), as is done in flux balance analysis. As long as we have some understanding of the properties of these parts, we can investigate whether their interaction leads to novel or unanticipated behaviour of the system that they constitute. There has been a tendency in the Systems Biology community to think that the collection and integration of data should continue ad infinitum, or that we will otherwise not be able to understand the systems that we study in their details. However, it may sometimes be useful to take a step back and consider whether the knowledge that we already have may not explain the system behaviour that we find so intriguing. Reasoning about systems can be difficult, and may require the application of mathematical techniques. The reward is sometimes the realization of unexpected conclusions, or in the worst case, that we still do not know enough details of the parts, or of the interactions between them. We will discuss a number of cases, with a focus on LAB-related work, where a typical systems approach has brought new knowledge or perspective, often counterintuitive, and clashing with conclusions from simpler approaches. Also novel types of testable hypotheses may be generated by the systems approach, which we will illustrate. Finally we will give an outlook on the fields of research where the systems approach may point the way for the near future.
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Affiliation(s)
- Bas Teusink
- Systems Bioinformatics/NISB, Faculty of Earth and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
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Abstract
Lactic acid bacteria are among the powerhouses of the food industry, colonize the surfaces of plants and animals, and contribute to our health and well-being. The genomic characterization of LAB has rocketed and presently over 100 complete or nearly complete genomes are available, many of which serve as scientific paradigms. Moreover, functional and comparative metagenomic studies are taking off and provide a wealth of insight in the activity of lactic acid bacteria used in a variety of applications, ranging from starters in complex fermentations to their marketing as probiotics. In this new era of high throughput analysis, biology has become big science. Hence, there is a need to systematically store the generated information, apply this in an intelligent way, and provide modalities for constructing self-learning systems that can be used for future improvements. This review addresses these systems solutions with a state of the art overview of the present paradigms that relate to the use of lactic acid bacteria in industrial applications. Moreover, an outlook is presented of the future developments that include the transition into practice as well as the use of lactic acid bacteria in synthetic biology and other next generation applications.
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Affiliation(s)
- Willem M de Vos
- Laboratory of Microbiology, Wageningen University, The Netherlands.
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