Phân tích so sánh vi sinh vật đường ruột tiết lộ khả năng giải độc amoniac và đồng hóa nitơ ở Cyprinus carpio var. specularis

Folia Microbiologica - Trang 1-13 - 2024
Chandni Talwar1,2, Shekhar Nagar1,3, Ram Krishan Negi1
1Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, India
2Department of Pathology & Immunology, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, USA
3Department of Zoology, Deshbandhu College, Kalkaji, India

Tóm tắt

Niche phức tạp của đường ruột cá thường được đặc trưng bởi các vi sinh vật liên quan có ý nghĩa trong liên kết sức khỏe đường ruột cá. Mặc dù những nỗ lực phân biệt cộng đồng vi sinh vật đã làm nổi bật cấu trúc khác biệt của chúng dọc theo chiều dài của đường ruột, thông tin về các hồ sơ cấu trúc và chức năng riêng biệt của chúng ở các phân đoạn đường ruột khác nhau ở nhiều loài cá vẫn còn rất hạn chế. Ở đây, chúng tôi đã thực hiện các phân tích phân loại so sánh và dự đoán chức năng của vi sinh vật ở phần ruột trước và ruột sau trong một loài cá nước ngọt ăn tạp, Cyprinus carpio var. specularis, thường được gọi là cá chép gương. Phân tích của chúng tôi cho thấy vi sinh vật ở ruột sau có thể được phân biệt với vi sinh vật ở ruột trước dựa trên sự phong phú của các vi khuẩn oxi hóa amoniac, khử nitrat và cố định nitơ thuộc về các họ như Rhodospirillaceae, Oxalobacteraceae, Nitrosomonadaceae và Nitrospiraceae. Về mặt chức năng, các con đường trao đổi chất độc đáo như phân hủy lignin, 2-nitrobenzoate, vanillin, vanillate và toluene được dự đoán trong ruột sau cũng gợi ý về khả năng của vi sinh vật ở ruột sau trong việc đồng hóa nitơ và giải độc amoniac. Nghiên cứu này làm nổi bật vai trò quan trọng của vi sinh vật ở ruột sau trong việc đồng hóa nitơ, vốn vẫn là một trong những chất dinh dưỡng hạn chế trong đường ruột của cá chép gương.

Từ khóa

#vi sinh vật đường ruột #cá chép gương #giải độc amoniac #đồng hóa nitơ #phân tích chức năng vi sinh vật

Tài liệu tham khảo

Arora PK, Sharma A (2015) New metabolic pathway for degradation of 2-nitrobenzoate by Arthrobacter sp. SPG. Front Microbiol 6551 Baldani JI, Rouws L, Cruz LM, Olivares FL, Schmid M, Hartmann A (2014) The family Oxalobacteraceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The Prokaryotes. Springer, Berlin, Heidelberg, Germany, pp 919–974 Banerjee G, Ray AK (2017) Bacterial symbiosis in the fish gut and its role in health and metabolism. Symbiosis 72:1–11 Baskaran V, Patil PK, Antony ML, Avunje S, Nagaraju VT, Ghate SD, Nathamuni S, Dineshkumar N, Alavandi SV, Vijayan KK (2020) Microbial community profiling of ammonia and nitrite oxidizing bacterial enrichments from brackishwater ecosystems for mitigating nitrogen species. Sci Rep 10:5201 Bauer MA, Kainz K, Carmona-Gutierrez D, Madeo F (2018) Microbial wars: competition in ecological niches and within the microbiome. Microb Cell 5:215–219 Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc 57:289–300 Bolyen E, Rideout JR, Dillon MR et al (2019) Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37:852–857 Bucking C, Wood CM (2012) Digestion of a single meal affects gene expression of ion and ammonia transporters and glutamine synthetase activity in the gastrointestinal tract of freshwater rainbow trout. J Comp Physiol B 182:341–350 Butt RL, Volkoff H (2019) Gut microbiota and energy homeostasis in fish. Front Endocrinol 10:9 Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP (2016) DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13:581–583 Chu BC, Garcia-Herrero A, Johanson TH, Krewulak KD, Lau CK, Peacock RS, Slavinskaya Z, Vogel HJ (2010) Siderophore uptake in bacteria and the battle for iron with the host; a bird’s eye view. Biometals 23:601–611 Daims H, Wagner M (2018) Nitrospira. Trends Microbiol 26462–463 Daims H (2014) The family Nitrospiraceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The Prokaryotes. Springer, Berlin, Heidelberg, Germany, pp 733–749 Das P, Babaei P, Nielsen J (2019) Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome. BMC Genom 20:208 de Bruijn I, Liu Y, Wiegertjes GF, Raaijmakers JM (2018) Exploring fish microbial communities to mitigate emerging diseases in aquaculture. FEMS Microbiol Ecol 94:fix161 DeSantis TZ, Hugenholtz P, Larsen N, Rojas M et al (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072 Douglas GM, Maffei VJ, Zaneveld J, Yurgel SN et al (2020) PICRUSt2 for prediction of metagenome functions. Nat Biotechnol 38:685–688 Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461 Egerton S, Culloty S, Whooley J, Stanton C, Ross RP (2018) The gut microbiota of marine fish. Front Microbiol 9:873 Ellermann M, Arthur JC (2017) Siderophore-mediated iron acquisition and modulation of host-bacterial interactions. Free Radic Biol Med 105:68–78 Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I Accuracy Assessment Genome Res 8:175–185 Fukami J, Cerezini P, Hungria M (2018) Azospirillum: benefits that go far beyond biological nitrogen fixation. AMB Express 8:73 Gonçalves AT, Gallardo-Escárate C (2017) Microbiome dynamic modulation through functional diets based on pre- and probiotics (mannan-oligosaccharides and Saccharomyces cerevisiae) in juvenile rainbow trout (Oncorhynchus mykiss). J Appl Microbiol 122:1333–1347 Görgényi J, Boros G, Vitál Z, Mozsár A, Várbíró G, Vasas G, Borics G (2016) The role of filter-feeding Asian carps in algal dispersion. Hydrobiologia 764:115–126 Han M, Yang K, Yang P, Zhong C, Chen C, Wang S, Lu Q, Ning K (2020) Stratification of athletes’ gut microbiota: the multifaceted hubs associated with dietary factors, physical characteristics and performance. Gut Microbes 12:1842991 Hira P, Bajaj A, Puri A, Talwar C et al (2019) Microbial genomics and metagenomics in India: explorations and perspectives. Proc Indian National Sci Acad 85:999–1023 Holmes AJ, Yi YV, Colakoglu F, Cliff JB, Klaassens E et al (2017) Diet-microbiome interactions in health are controlled by intestinal nitrogen source constraints. Cell Metab 25:140–151 Ikeda-Ohtsubo W, Brugman S, Warden CH, Rebel JMJ, Folkerts G, Pieterse CMJ (2018) How can we define “Optimal Microbiota?”: a comparative review of structure and functions of microbiota of animals, fish, and plants in agriculture. Front Nutr 5:90 Irazoki O, Hernandez SB, Cava F (2019) Peptidoglycan muropeptides: release, perception, and functions as signaling molecules. Front Microbiol 10:500 Jami M, Ghanbari M, Kneifel W, Domig KJ (2015) Phylogenetic diversity and biological activity of culturable Actinobacteria isolated from freshwater fish gut microbiota. Microbiol Res 175:6–15 Kolde R, Kolde MR (2015) Package ‘pheatmap’. R package 1:790. https://cran.rproject.org/web/packages/pheatmap/pheatmap.pdf Kreuzer M, Heindl U, Roth-Maier DA, Kirchgessner M (1991) Cellulose fermentation capacity of the hindgut and nitrogen turnover in the hindgut of sows as evaluated by oral and intracecal supply of purified cellulose. Arch Anim Nutr 41:359–372 Ktari N, Jridi M, Bkhairia I, Sayari N, Ben Salah R, Nasri M (2012) Functionalities and antioxidant properties of protein hydrolysates from muscle of zebra blenny (Salaria basilisca) obtained with different crude protease extracts. Food Res Intl 49:747–756 Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R (2011) Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Bioinformatics 10:10 Kulichevskaya IS, Naumoff DG, Miroshnikov KK, Ivanova AA et al (2020) Limnoglobus roseus gen. nov., sp. nov., a novel freshwater planctomycete with a giant genome from the family Gemmataceae. Intl J Syst Evol Microbiol 70:1240–1249 Kulichevskaya IS, Serkebaeva YM, Kim Y, Rijpstra WIC, Damsté JSS, Liesack W, Dedysh SN (2012) Telmatocola sphagniphila gen. nov., sp. nov., a novel dendriform planctomycete from northern wetlands. Front Microbiol 3:146 Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874 Le MH, Wang D (2020) Structure and membership of gut microbial communities in multiple fish cryptic species under potential migratory effects. Sci Rep 10:7547 Le HT, Shao X, Krogdahl Å, Kortner TM, Lein I, Kousoulaki K, Lie KK, Sæle Ø (2019) Intestinal function of the stomachless fish, Ballan Wrasse (Labrus bergylta). Front Mar Sci 6:140 Leahy JG, Olsen RH (1997) Kinetics of toluene degradation by toluene-oxidizing bacteria as a function of oxygen concentration, and the effect of nitrate. FEMS Microbiol Ecol 23:23–30 Lee C, Park C (2017) Bacterial responses to glyoxal and methylglyoxal: reactive electrophilic species. Int J Mol Sci 18:E169 Lewin WC, Kamjunke N, Mehner T (2003) Phosphorus uptake by Microcystis during passage through fish guts. Limnol Oceanogr 48:2392–2396 Li XM, Zhu YJ, Yan QY, Ringø E, Yang DG (2014) Do the intestinal microbiotas differ between paddlefish (Polyodon spathala) and bighead carp (Aristichthys nobilis) reared in the same pond. J Appl Microbiol 117:1245–1252 Liu H, Guo X, Gooneratne R, Lai R, Zeng C, Zhan F, Wang W (2016) The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels. Sci Rep 6:24340 Llewellyn MS, Boutin S, Hoseinifar SH, Derome N (2014) Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries. Front Microbiol 5:207 Madigan M, Cox SS, Stegeman RA (1984) Nitrogen fixation and nitrogenase activities in members of the family Rhodospirillaceae. J Bacteriol 157:73–78 McDonald R, Zhang F, Watts JE, Schreier HJ (2015) Nitrogenase diversity and activity in the gastrointestinal tract of the wood-eating catfish Panaque nigrolineatus. ISME J 9:2712–2724 McIlroy SJ, Nielsen PH (2014) The family Saprospiraceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The Prokaryotes. Springer, Berlin, Heidelberg, Germany, pp 863–889 McMurdie PJ, Holmes S (2014) Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol 10:e1003531 Mitchell AM, Srikumar T, Silhavy TJ (2018) Cyclic Enterobacterial common antigen maintains the outer membrane permeability barrier of Escherichia coli in a manner controlled by YhdP. Mbio 9:e01321-e1418 Nagar S, Talwar C, Bharti M, Yadav S, Siwach S, Negi RK (2021) Metagenome-assembled genomes recovered from the datasets of a high-altitude Himalayan hot spring Khirganga, Himachal Pradesh. India DIB 39:107551 Nagar S, Bharti M, Negi RK (2023) Genome-resolved metagenomics revealed metal-resistance, geochemical cycles in a Himalayan hot spring. Appl Microbiol Biotechnol 107:3273–3289 Nielsen S, Walburn JW, Vergés A, Thomas T, Egan S (2017) Microbiome patterns across the gastrointestinal tract of the rabbitfish Siganus fuscescens. PeerJ 5:e3317 Ohkuma M, Noda S, Kudo T (1999) Phylogenetic diversity of nitrogen fixation genes in the symbiotic microbial community in the gut of diverse termites. Appl Environ Microbiol 65:4926–4934 Oren A, Xu XW (2014) The family Hyphomicrobiaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The Prokaryotes. Springer, Berlin, Heidelberg, Germany, pp 247–281 Parata L, Nielsen S, Xing X, Thomas T, Egan S, Vergés A (2020) Age, gut location and diet impact the gut microbiome of a tropical herbivorous surgeonfish. FEMS Microbiol Ecol 96:fiz179 Parks DH, Beiko RG (2010) Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26:715–721 Perna S, Alalwan TA, Alaali Z, Alnashaba T, Gasparri C et al (2019) The role of glutamine in the complex interaction between gut microbiota and health: a narrative review. Intl J Mol Sci 20:5232 Perry WB, Lindsay E, Payne CJ, Brodie C, Kazlauskaite R (2020) The role of the gut microbiome in sustainable teleost aquaculture. Proc Royal Soc B 287:20200184 Prosser JI, Head IM, Stein LY (2014) The family Nitrosomonadaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The Prokaryotes. Springer, Berlin, Heidelberg, Germany, pp 901–918 Pujalte MJ, Lucena T, Ruvira MA, Arahal DR, Macián MC (2014) The family Rhodobacteraceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The Prokaryotes. Springer, Berlin, Heidelberg, Germany, pp 439–512 Rahman MM (2015) Effects of co-cultured common carp on nutrients and food web dynamics in rohu aquaculture ponds. Aquac Environ Interact 6:223–232 Ramos-Molina B, Queipo-Ortuño MI, Lambertos A, Tinahones FJ, Peñafiel R (2019) Dietary and gut microbiota polyamines in obesity- and age-related diseases. Front Nutr 6:24 Ravin NV, Rakitin AL, Ivanova AA, Beletsky AV, Kulichevskaya IS, Mardanov AV, Dedysh SN (2018) Genome analysis of Fimbriiglobus ruber SP5T, a planctomycete with confirmed chitinolytic capability. Appl Environ Microbiol 84:AEM.0264545-17 Reese AT, Pereira FC, Schintlmeister A, Berry D et al (2018) Microbial nitrogen limitation in the mammalian large intestine. Nat Microbiol 3:1441–1450 Rekdal VM, Bernadino PN, Luescher MU et al (2020) A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols. Elife 9:e50845 Ringø E, Zhou Z, Vecino J, Wadsworth S, Romero J et al (2016) Effect of dietary components on the gut microbiota of aquatic animals. Aquac Nutr 22:219–282 Sabree ZL, Moran NA (2014) Host-specific assemblages typify gut microbial communities of related insect species. Springerplus 3:138 Shannon P, Markiel A, Ozier O, Baliga NS et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504 Smith LS (1980) Digestion in teleost fishes. Fish feeds technology AO/UNDP Aquaculture Development and Coordination Programme Rome 3–18 Steenhoudt O, Vanderleyden J (2000) Azospirillum, a free-living nitrogen-fixing bacterium closely associated with grasses: genetic, biochemical and ecological aspects. FEMS Microbiol Rev 24:487–506 Sullam KE, Essinger SD, Lozupone CA, O’Connor MP et al (2012) Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis. Mol Ecol 21:3363–3378 Talwar C, Nagar S, Lal R, Negi RK (2018) Fish gut microbiome: current approaches and future perspectives. Indian J Microbiol 58:397–414 Talwar C, Singh AK, Choksket S, Korpole S, Lal R, Negi RK (2020) Salinicoccus cyprini sp. nov., isolated from the gut of mirror carp, Cyprinus carpio var. specularis. Intl J Sys Evol Microbiol 70:4111–4118 Wang AR, Ran C, Ringø E, Zhou ZG (2018) Progress in fish gastrointestinal microbiota research. Rev Aquac 10:626–640 Weber MJ, Brown ML (2011) Relationships among invasive common carp, native fishes, and physicochemical characteristics in upper Midwest (USA) lakes. Ecol Freshw Fish 20:270–278 Xu Z, Lei P, Zhai R, Wen Z, Jin M (2019) Recent advances in lignin valorization with bacterial cultures: microorganisms, metabolic pathways, and bio-products. Biotechnol Biofuels 12:32 Yan Q, Li J, Yu Y, Wang J, He Z, Van Nostrand JD, Kempher ML, Wu L, Wang Y, Liao L, Li X (2016) Environmental filtering decreases with fish development for the assembly of gut microbiota. Environ Microbiol 12:4739–4754 Ye L, Amberg J, Chapman D, Gaikowski M, Liu WT (2014) Fish gut microbiota analysis differentiates physiology and behavior of invasive Asian carp and indigenous American fish. ISME J 8:541–551 Yu H, Guo Z, Shen S, Shan W (2016) Effects of taurine on gut microbiota and metabolism in mice. Amino Acids 48:1601–1617 Zeng A, Tan K, Gong P, Lei P, Guo Z (2020) Correlation of microbiota in the gut of fish species and water. 3 Biotech 10:472