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

Chapter  Google Scholar 

Banerjee G, Ray AK (2017) Bacterial symbiosis in the fish gut and its role in health and metabolism. Symbiosis 72:1–11

Article  CAS  Google Scholar 

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

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

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

Article  PubMed  PubMed Central  Google Scholar 

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

MathSciNet  Google Scholar 

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

Article  CAS  PubMed  PubMed Central  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

Butt RL, Volkoff H (2019) Gut microbiota and energy homeostasis in fish. Front Endocrinol 10:9

Article  Google Scholar 

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

Article  CAS  PubMed  PubMed Central  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Chapter  Google Scholar 

Das P, Babaei P, Nielsen J (2019) Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome. BMC Genom 20:208

Article  Google Scholar 

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

Article  Google Scholar 

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

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

Douglas GM, Maffei VJ, Zaneveld J, Yurgel SN et al (2020) PICRUSt2 for prediction of metagenome functions. Nat Biotechnol 38:685–688

Article  CAS  PubMed  PubMed Central  Google Scholar 

Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461

Article  CAS  PubMed  Google Scholar 

Egerton S, Culloty S, Whooley J, Stanton C, Ross RP (2018) The gut microbiota of marine fish. Front Microbiol 9:873

Article  PubMed  PubMed Central  Google Scholar 

Ellermann M, Arthur JC (2017) Siderophore-mediated iron acquisition and modulation of host-bacterial interactions. Free Radic Biol Med 105:68–78

Article  CAS  PubMed  Google Scholar 

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

CAS  PubMed  Google Scholar 

Fukami J, Cerezini P, Hungria M (2018) Azospirillum: benefits that go far beyond biological nitrogen fixation. AMB Express 8:73

Article  PubMed  PubMed Central  Google Scholar 

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

Article  PubMed  Google Scholar 

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

Article  Google Scholar 

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

Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  PubMed  PubMed Central  Google Scholar 

Irazoki O, Hernandez SB, Cava F (2019) Peptidoglycan muropeptides: release, perception, and functions as signaling molecules. Front Microbiol 10:500

Article  PubMed  PubMed Central  Google Scholar 

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

Article  PubMed  Google Scholar 

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

CAS  Google Scholar 

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

Article  CAS  Google Scholar 

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

Google Scholar 

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

Article  CAS  Google Scholar 

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

Article  PubMed  PubMed Central  Google Scholar 

Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

Article  CAS  PubMed  PubMed Central  Google Scholar 

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

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

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

Article  Google Scholar 

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

Article  CAS  Google Scholar 

Lee C, Park C (2017) Bacterial responses to glyoxal and methylglyoxal: reactive electrophilic species. Int J Mol Sci 18:E169

Article  Google Scholar 

Lewin WC, Kamjunke N, Mehner T (2003) Phosphorus uptake by Microcystis during passage through fish guts. Limnol Oceanogr 48:2392–2396

Article  ADS  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

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

Article  ADS