referencing style?

Hi team
I found Scientific Reports J referencing style not working consistenly in the biobliography
so there is different styles used as below.
https://s3.amazonaws.com/zotero.org/images/forums/u11191304/3fbcnab0ghaaz7fy62cw.png
Here (https://www.nature.com/srep/author-instructions/submission-guidelines#references) is the style of scientiifc reports mentioned
https://s3.amazonaws.com/zotero.org/images/forums/u11191304/zadd0yw81zcpft06i1sj.png
  • You mean the DOI in 20? That's on purpose and as per requirement for articles without volume (typically 'online first' pieces)
  • not sure what is on-purpose
    the list have differences in the style even when the volume is available (if I get your point correctly)
    1. Reverter, M., Tapissier-Bontemps, N., Sarter, S., Sasal, P. & Caruso, D. Moving towards more sustainable aquaculture practices: a meta-analysis on the potential of plant-enriched diets to improve fish growth, immunity and disease resistance. Rev. Aquac. 13, 537–555 (2021).
    2. Espe, M., Lemme, A., Petri, A. & El-Mowafi, A. Can Atlantic salmon (Salmo salar) grow on diets devoid of fish meal? Aquaculture 255, 255–262 (2006).
    3. Conceição, L. E. C. et al. Novel methodologies in marine fish larval nutrition. Fish Physiol. Biochem. 36, 1–16 (2010).
    4. Hou, Z. & Fuiman, L. A. Nutritional programming in fishes: insights from mammalian studies. Rev. Fish Biol. Fish. 30, 67–92 (2020).
    5. Moghadam, H., Mørkøre, T. & Robinson, N. Epigenetics—Potential for Programming Fish for Aquaculture? J. Mar. Sci. Eng. 3, 175–192 (2015).
    6. Banerjee, G. & Ray, A. K. Bacterial symbiosis in the fish gut and its role in health and metabolism. Symbiosis 72, 1–11 (2017).
    7. Ray, A. k., Ghosh, K. & Ringø, E. Enzyme-producing bacteria isolated from fish gut: a review. Aquac. Nutr. 18, 465–492 (2012).
    8. Xiong, J.-B., Nie, L. & Chen, J. Current understanding on the roles of gut microbiota in fish disease and immunity. Zool. Res. 40, 70–76 (2019).
    9. Yukgehnaish, K. et al. Gut microbiota metagenomics in aquaculture: factors influencing gut microbiome and its physiological role in fish. Rev. Aquac. 12, 1903–1927 (2020).
    10. Desai, A. R. et al. Effects of plant-based diets on the distal gut microbiome of rainbow trout (Oncorhynchus mykiss). Aquaculture 350–353, 134–142 (2012).
    11. Gajardo, K. et al. Alternative Protein Sources in the Diet Modulate Microbiota and Functionality in the Distal Intestine of Atlantic Salmon (Salmo salar). Appl. Environ. Microbiol. 83, e02615-16 (2017).
    12. Miao, S. et al. Dietary soybean meal affects intestinal homoeostasis by altering the microbiota, morphology and inflammatory cytokine gene expression in northern snakehead. Sci. Rep. 8, 113 (2018).
    13. Wang, J. et al. Effects of fish meal replacement by soybean meal with supplementation of functional compound additives on intestinal morphology and microbiome of Japanese seabass (Lateolabrax japonicus). Aquac. Res. 48, 2186–2197 (2017).
    14. Rimoldi, S., Terova, G., Ascione, C., Giannico, R. & Brambilla, F. Next generation sequencing for gut microbiome characterization in rainbow trout (Oncorhynchus mykiss) fed animal by-product meals as an alternative to fishmeal protein sources. PLOS ONE 13, e0193652 (2018).
    15. Schmidt, V., Amaral-Zettler, L., Davidson, J., Summerfelt, S. & Good, C. Influence of Fishmeal-Free Diets on Microbial Communities in Atlantic Salmon (Salmo salar) Recirculation Aquaculture Systems. Appl. Environ. Microbiol. 82, 4470–4481 (2016).
    16. Yang, C., Jiang, M., Lu, X. & Wen, H. Effects of Dietary Protein Level on the Gut Microbiome and Nutrient Metabolism in Tilapia (Oreochromis niloticus). Animals 11, 1024 (2021).
    17. Green, T. J., Smullen, R. & Barnes, A. C. Dietary soybean protein concentrate-induced intestinal disorder in marine farmed Atlantic salmon, Salmo salar is associated with alterations in gut microbiota. Vet. Microbiol. 166, 286–292 (2013).
    18. Hartviksen, M. et al. Alternative dietary protein sources for Atlantic salmon (Salmo salar L.) effect on intestinal microbiota, intestinal and liver histology and growth. Aquac. Nutr. 20, 381–398 (2014).
    19. Martinez-Guryn, K., Leone, V. & Chang, E. B. Regional Diversity of the Gastrointestinal Microbiome. Cell Host Microbe 26, 314–324 (2019).
    20. McCallum, G. & Tropini, C. The gut microbiota and its biogeography. Nat. Rev. Microbiol. 1–14 (2023) doi:10.1038/s41579-023-00969-0.
    21. Ringø, E. et al. Effect of dietary components on the gut microbiota of aquatic animals. A never-ending story? Aquac. Nutr. 22, 219–282 (2016).
    22. Kwasek, K. et al. The Effect of First Feeding Exposure of Larval Largemouth Bass to a Formulated Soybean Meal-Based or Soy Saponin-Supplemented Diet on Fish Growth Performance and Gut Microbiome. North Am. J. Aquac. 83, 312–326 (2021).
    23. Kwasek, K. et al. Does Exposure of Broodstock to Dietary Soybean Meal Affect Its Utilization in the Offspring of Zebrafish (Danio rerio)? Animals 12, 1475 (2022).
    24. Michl, S. C. et al. The malleable gut microbiome of juvenile rainbow trout (Oncorhynchus mykiss): Diet-dependent shifts of bacterial community structures. PLOS ONE 12, e0177735 (2017).
    25. Michl, S. C. et al. A diet-change modulates the previously established bacterial gut community in juvenile brown trout (Salmo trutta). Sci. Rep. 9, 2339 (2019).
    26. Patula, S. et al. Nutritional Programming with Dietary Soybean Meal and Its Effect on Gut Microbiota in Zebrafish (Danio rerio). Zebrafish 18, 125–138 (2021).
    27. McMillan, S. et al. Can nutritional programming in Atlantic salmon (Salmo salar) be optimised with a reduced stimulus period? Aquaculture 585, 740686 (2024).
    28. Dehler, C. E., Secombes, C. J. & Martin, S. A. M. Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.). Aquaculture 467, 149–157 (2017).
    29. Klindworth, A. et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41, e1 (2013).
    30. Lorgen-Ritchie, M. et al. A Temporally Dynamic Gut Microbiome in Atlantic Salmon During Freshwater Recirculating Aquaculture System (RAS) Production and Post-seawater Transfer. Front. Mar. Sci. 8, (2021).
    31. Krueger, F. et al. FelixKrueger/TrimGalore: v0.6.10. Zenodo https://doi.org/10.5281/zenodo.7598955 (2023).
    32. Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10–12 (2011).
    33. Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
    34. Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590-596 (2013).
    35. Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A. & Callahan, B. J. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome 6, 226 (2018).
    36. Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014).
    37. Heidrich, V., Karlovsky, P. & Beule, L. ‘SRS’ R Package and ‘q2-srs’ QIIME 2 Plugin: Normalization of Microbiome Data Using Scaling with Ranked Subsampling (SRS). Appl. Sci. 11, 11473 (2021).
    38. Liu, C., Cui, Y., Li, X. & Yao, M. microeco: an R package for data mining in microbial community ecology. FEMS Microbiol. Ecol. 97, fiaa255 (2021).
    39. McMurdie, P. J. & Holmes, S. phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLOS ONE 8, e61217 (2013).


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    50. Navarrete, P., Espejo, R. T. & Romero, J. Molecular Analysis of Microbiota Along the Digestive Tract of Juvenile Atlantic Salmon (Salmo salar L.). Microb. Ecol. 57, 550–561 (2009).
    51. Geurden, I. et al. High or low dietary carbohydrate:protein ratios during first-feeding affect glucose metabolism and intestinal microbiota in juvenile rainbow trout. J. Exp. Biol. 217, 3396–3406 (2014).
    52. Castañeda-Monsalve, V. A., Junca, H., García-Bonilla, E., Montoya-Campuzano, O. I. & Moreno-Herrera, C. X. Characterization of the gastrointestinal bacterial microbiome of farmed juvenile and adult white Cachama (Piaractus brachypomus). Aquaculture 512, 734325 (2019).
    53. Feng, W. et al. Gut segments outweigh the diet in shaping the intestinal microbiota composition in grass carp Ctenopharyngodon idellus. AMB Express 9, 44 (2019).
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  • I'm not going through 80 references. Can you just tell me what you think is wrong/inconsistent?
  • i am not asking to go through them
    i just scanned them by eye in few seconds and as I mentioned earlier they are inconsistent having et al or doesn't for no reason that I can see. Your earlier reply doesn't make sense. zotero need to fix this I think or clarify. cheers

  • You didn't say anything about et al before and the style does use this consistently for references with 6 or more authors. If you have any reason to believe that's incorrect, you can say that. FWIW there's is a Nature style without et al available https://www.zotero.org/styles?q=id:nature-no-et-al&dependent=0
  • sorry
    thanks
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