Profiling of d-alanine production by the microbial isolates of rat gut microbiota.
amino acid
gastrointestinal microbiome
host microbial interactions
mass spectrometry
rats
Journal
FASEB journal : official publication of the Federation of American Societies for Experimental Biology
ISSN: 1530-6860
Titre abrégé: FASEB J
Pays: United States
ID NLM: 8804484
Informations de publication
Date de publication:
08 2022
08 2022
Historique:
revised:
07
06
2022
received:
03
11
2021
accepted:
27
06
2022
entrez:
11
7
2022
pubmed:
12
7
2022
medline:
14
7
2022
Statut:
ppublish
Résumé
d-alanine (d-Ala) and several other d-amino acids (d-AAs) act as hormones and neuromodulators in nervous and endocrine systems. Unlike the endogenously synthesized d-serine in animals, d-Ala may be from exogenous sources, e.g., diet and intestinal microorganisms. However, it is unclear if the capability to produce d-Ala and other d-AAs varies among different microbial strains in the gut. We isolated individual microorganisms of rat gut microbiota and profiled their d-AA production in vitro, focusing on d-Ala. Serial dilutions of intestinal contents from adult male rats were plated on agar to obtain clonal cultures. Using MALDI-TOF MS for rapid strain typing, we identified 38 unique isolates, grouped into 11 species based on 16S rRNA gene sequences. We then used two-tier screening to profile bacterial d-AA production, combining a d-amino acid oxidase-based enzymatic assay for rapid assessment of non-acidic d-AA amount and chiral LC-MS/MS to quantify individual d-AAs, revealing 19 out of the 38 isolated strains as d-AA producers. LC-MS/MS analysis of the eight top d-AA producers showed high levels of d-Ala in all strains tested, with substantial inter- and intra-species variations. Though results from the enzymatic assay and LC-MS/MS analysis aligned well, LC-MS/MS further revealed the existence of d-glutamate and d-aspartate, which are poor substrates for this enzymatic assay. We observed large inter- and intra-species variation of d-AA production profiles from rat gut microbiome species, demonstrating the importance of chemical profiling of gut microbiota in addition to sequencing, furthering the idea that microbial metabolites modulate host physiology.
Identifiants
pubmed: 35816159
doi: 10.1096/fj.202101595R
doi:
Substances chimiques
Amino Acids
0
RNA, Ribosomal, 16S
0
Alanine
OF5P57N2ZX
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e22446Informations de copyright
© 2022 The Authors. The FASEB Journal published by Wiley Periodicals LLC on behalf of Federation of American Societies for Experimental Biology.
Références
Liu Y, Hou Y, Wang G, Zheng X, Hao H. Gut microbial metabolites of aromatic amino acids as signals in host-microbe interplay. Trends Endocrinol Metab. 2020;31(11):818-834.
Koh A, De Vadder F, Kovatcheva-Datchary P, Bäckhed F. From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell. 2016;165(6):1332-1345.
Rastelli M, Cani PD, Knauf C. The gut microbiome influences host endocrine functions. Endocr Rev. 2019;40(5):1271-1284.
Strandwitz P. Neurotransmitter modulation by the gut microbiota. Brain Res. 2018;1693(Pt B):128-133.
Ishii C, Furusho A, Hsieh C-L, Hamase K. Multi-dimensional high-performance liquid chromatographic determination of chiral amino acids and related compounds in real world samples. Chromatography. 2020;41(1):1-17.
Wolosker H, Dumin E, Balan L, Foltyn VN. D-amino acids in the brain: D-serine in neurotransmission and neurodegeneration. FEBS J. 2008;275(14):3514-3526.
Lockridge AD, Baumann DC, Akhaphong B, Abrenica A, Miller RF, Alejandro EU. Serine racemase is expressed in islets and contributes to the regulation of glucose homeostasis. Islets. 2016;8(6):195-206.
Mothet J-P, Le Bail M, Billard J-M. Time and space profiling of NMDA receptor co-agonist functions. J Neurochem. 2015;135(2):210-225.
D'Aniello A, Di Fiore MM, Fisher GH, et al. Occurrence of D-aspartic acid and N-methyl-D-aspartic acid in rat neuroendocrine tissues and their role in the modulation of luteinizing hormone and growth hormone release. FASEB J. 2000;14(5):699-714.
Furuchi T, Homma H. Free D-aspartate in mammals. Biol Pharm Bull. 2005;28(9):1566-1570.
Roshanzamir F, Safavi SM. The putative effects of D-Aspartic acid on blood testosterone levels: A systematic review. Int J Reprod Biomed. 2017;15(1):1-10.
Morikawa A, Hamase K, Ohgusu T, et al. Immunohistochemical localization of D-alanine to beta-cells in rat pancreas. Biochem Biophys Res Commun. 2007;355(4):872-876.
Etoh S, Hamase K, Morikawa A, Ohgusu T, Zaitsu K. Enantioselective visualization of D-alanine in rat anterior pituitary gland: localization to ACTH-secreting cells. Anal Bioanal Chem. 2009;393(1):217-223.
Ota N, Rubakhin SS, Sweedler JV. d-Alanine in the islets of Langerhans of rat pancreas. Biochem Biophys Res Commun. 2014;447(2):328-333.
Wang L, Ota N, Romanova EV, Sweedler JV. A novel pyridoxal 5′-phosphate-dependent amino acid racemase in the Aplysia californica central nervous system. J Biol Chem. 2011;286(15):13765-13774.
Kim PM, Duan X, Huang AS, et al. Aspartate racemase, generating neuronal D-aspartate, regulates adult neurogenesis. Proc Natl Acad Sci U S A. 2010;107(7):3175-3179.
Marcone GL, Rosini E, Crespi E, Pollegioni L. D-amino acids in foods. Appl Microbiol Biotechnol. 2020;104(2):555-574.
Bastings JJAJ, van Eijk HM, Olde Damink SW, Rensen SS. d-amino Acids in health and disease: a focus on cancer. Nutrients. 2019;11(9):2205.
Cava F, Lam H, de Pedro MA, Waldor MK. Emerging knowledge of regulatory roles of d-amino acids in bacteria. Cell Mol Life Sci. 2011;68(5):817-831.
Karakawa S, Miyoshi Y, Konno R, et al. Two-dimensional high-performance liquid chromatographic determination of day-night variation of D-alanine in mammals and factors controlling the circadian changes. Anal Bioanal Chem. 2013;405(25):8083-8091.
Qin J, Li Y, Cai Z, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012;490(7418):55-60.
Sasabe J, Miyoshi Y, Rakoff-Nahoum S, et al. Interplay between microbial d-amino acids and host d -amino acid oxidase modifies murine mucosal defence and gut microbiota. Nat Microbiol. 2016;1(10):1-7.
Lee RJ, Hariri BM, McMahon DB, et al. Bacterial d-amino acids suppress sinonasal innate immunity through sweet taste receptors in solitary chemosensory cells. Sci Signal. 2017;10(495):eaam7703.
Holmes E, Li JV, Marchesi JR, Nicholson JK. Gut microbiota composition and activity in relation to host metabolic phenotype and disease risk. Cell Metab. 2012;16(5):559-564.
Lam H, Oh D-C, Cava F, et al. D-amino acids govern stationary phase cell wall remodeling in bacteria. Science. 2009;325(5947):1552-1555.
Patnode ML, Guruge JL, Castillo JJ, et al. Strain-level functional variation in the human gut microbiota based on bacterial binding to artificial food particles. Cell Host Microbe. 2021;29(4):664-673.e665.
Yang C, Mogno I, Contijoch EJ, et al. Fecal IgA levels are determined by strain-level differences in bacteroides ovatus and are modifiable by gut microbiota manipulation. Cell Host Microbe. 2020;27(3):467-475.e466.
Laubach T, von Haeseler A, Lercher MJ. TreeSnatcher plus: capturing phylogenetic trees from images. BMC Bioinformatics. 2012;13(1):110.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35(6):1547-1549.
Dione N, Khelaifia S, La Scola B, Lagier JC, Raoult D. A quasi-universal medium to break the aerobic/anaerobic bacterial culture dichotomy in clinical microbiology. Clin Microbiol Infect. 2016;22(1):53-58.
Lee CJ, Qiu TA, Sweedler JV. d-Alanine: Distribution, origin, physiological relevance, and implications in disease. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 2020;1868(11):140482.
Matsumoto M, Kunisawa A, Hattori T, et al. Free D -amino acids produced by commensal bacteria in the colonic lumen. Sci Rep. 2018;8(1):17915.
Li D, Chen H, Mao B, et al. Microbial biogeography and core microbiota of the rat digestive tract. Sci Rep. 2017;8:45840.
Rosini E, Caldinelli L, Piubelli L. Assays of D-amino acid oxidase activity. Front Mol Biosci. 2018;4:102.
Hernández SB, Cava F. Environmental roles of microbial amino acid racemases. Environ Microbiol. 2016;18(6):1673-1685.
Trachtenberg S. Mollicutes-wall-less bacteria with internal cytoskeletons. J Struct Biol. 1998;124(2):244-256.
Pollegioni L, Molla G. New biotech applications from evolved D-amino acid oxidases. Trends Biotechnol. 2011;29(6):276-283.
Rosini E, D'Antona P, Pollegioni L. Biosensors for D-amino acids: detection methods and applications. Int J Mol Sci. 2020;21(13):4574.
Suzuki M, Sujino T, Chiba S, et al. Host-microbe cross-talk governs amino acid chirality to regulate survival and differentiation of B cells. Sci Adv. 2021;7(10):eabd6480.
Kuleshov V, Jiang C, Zhou W, Jahanbani F, Batzoglou S, Snyder M. Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Nat Biotechnol. 2016;34(1):64-69.
Mortuza R. Thesis: Phenotypic and Molecular Analysis of the Alanine and Glutamate Racemases of Mycobacteria. University of Otago; 2017.
Krause K, Poen S, Mortuza R, et al. Glutamate racemase from Mycobacterium tuberculosis: new genetic and structural insights into a target for antituberculosis drug design. Open Forum Infect Dis. 2015;2(suppl_1):881.
Krämer R. Secretion of amino acids by bacteria: physiology and mechanism. FEMS Microbiol Rev. 1994;13(1):75-93.
Percy MG, Gründling A. Lipoteichoic acid synthesis and function in gram-positive bacteria. Annu Rev Microbiol. 2014;68(1):81-100.
Chesnokova ON, McPherson SA, Steichen CT, Turnbough CL. The spore-specific alanine racemase of Bacillus anthracis and its role in suppressing germination during spore development. J Bacteriol. 2009;191(4):1303-1310.
Preston RA, Douthit HA. Germination of Bacillus cereus spores: critical control by DL-alanine racemase. Microbiology. 1984;130(12):3123-3133.
Fox A, Black GE, Fox K, Rostovtseva S. Determination of carbohydrate profiles of Bacillus anthracis and Bacillus cereus including identification of O-methyl methylpentoses by using gas chromatography-mass spectrometry. J Clin Microbiol. 1993;31(4):887-894.
Leoff C, Saile E, Sue D, et al. Cell wall carbohydrate compositions of strains from the Bacillus cereus group of species correlate with phylogenetic relatedness. J Bacteriol. 2008;190(1):112-121.
Choudhury B, Leoff C, Saile E, et al. The structure of the major cell wall polysaccharide of bacillus anthracis is species-specific. J Biol Chem. 2006;281(38):27932-27941.
Dodd D, Reese JG, Louer CR, Ballard JD, Spies MA, Blanke SR. Functional comparison of the two Bacillus anthracis glutamate racemases. J Bacteriol. 2007;189(14):5265-5275.
Kajitani K, Ishikawa T, Shibata K, Kouya T, Kera Y, Takahashi S. Development of an enzymatic screening method for d-aspartate-producing lactic acid bacteria. Enzyme Microb Technol. 2021;149:109835.
Reynolds PE, Courvalin P. Vancomycin resistance in Enterococci due to synthesis of precursors terminating in d-Alanyl-d-Serine. Antimicrob Agents Chemother. 2005;49(1):21-25.
Sieradzki K, Tomasz A. A highly vancomycin-resistant laboratory mutant of Staphylococcus aureus. FEMS Microbiol Lett. 1996;142(2-3):161-166.
Veiga P, Piquet S, Maisons A, et al. Identification of an essential gene responsible for D-Asp incorporation in the Lactococcus lactis peptidoglycan crossbridge. Mol Microbiol. 2006;62(6):1713-1724.
Bellais S, Arthur M, Dubost L, et al. Aslfm, the D-aspartate ligase responsible for the addition of D-aspartic acid onto the peptidoglycan precursor of Enterococcus faecium. J Biol Chem. 2006;281(17):11586-11594.
Zeng D, Debabov D, Hartsell TL, et al. Approved glycopeptide antibacterial drugs: mechanism of action and resistance. Cold Spring Harb Perspect Med. 2016;6(12):a026989.
Lin C-H, Yang H-T, Chiu C-C, Lane H-Y. Blood levels of D-amino acid oxidase vs. D-amino acids in reflecting cognitive aging. Sci Rep. 2017;7(1):14849.
Lin C-H, Yang H-T, Lane H-Y. D-glutamate, D-serine, and D-alanine differ in their roles in cognitive decline in patients with Alzheimer's disease or mild cognitive impairment. Pharmacol Biochem Behav. 2019;185:172760.
Chang C-H, Lin C-H, Liu C-Y, et al. Plasma d-glutamate levels for detecting mild cognitive impairment and Alzheimer's disease: machine learning approaches. J Psychopharmacol. 2021;35(3):265-272.
Wong D, Atiya S, Fogarty J, et al. Reduced hippocampal glutamate and posterior cingulate N-acetyl aspartate in mild cognitive impairment and Alzheimer's disease is associated with episodic memory performance and white matter integrity in the cingulum: a pilot study. J Alzheimers Dis. 2020;73(4):1385-1405.
Seckler JM, Lewis SJ. Advances in D-amino acids in neurological research. Int J Mol Sci. 2020;21(19):7325.
Hamasu K, Shigemi K, Tsuneyoshi Y, et al. Intracerebroventricular injection of L-proline and D-proline induces sedative and hypnotic effects by different mechanisms under an acute stressful condition in chicks. Amino Acids. 2010;38(1):57-64.
Horio M, Kohno M, Fujita Y, et al. Levels of D-serine in the brain and peripheral organs of serine racemase (Srr) knock-out mice. Neurochem Int. 2011;59(6):853-859.
Savignac HM, Corona G, Mills H, et al. Prebiotic feeding elevates central brain derived neurotrophic factor, N-methyl-d-aspartate receptor subunits and d-serine. Neurochem Int. 2013;63(8):756-764.
Nakade Y, Iwata Y, Furuichi K, et al. Gut microbiota-derived D-serine protects against acute kidney injury. JCI Insight. 2018;3(17):e97957.
Kawase T, Nagasawa M, Ikeda H, Yasuo S, Koga Y, Furuse M. Gut microbiota of mice putatively modifies amino acid metabolism in the host brain. Br J Nutr. 2017;117(6):775-783.
Aliashkevich A, Alvarez L, Cava F. New insights into the mechanisms and biological roles of D-amino acids in complex eco-systems. Front Microbiol. 2018;9:683.
Sela U, Euler CW, Rosa JC, Fischetti VA. Strains of bacterial species induce a greatly varied acute adaptive immune response: the contribution of the accessory genome. PLoS Pathog. 2018;14(1):e1006726.