docs(paper): rewrite manuscript and update bibliography

paper/paper.bib

@@ -147,4 +147,68 @@ @article{Waskom2021
   year      = {2021},
   doi       = {10.21105/joss.03021},
   url       = {https://doi.org/10.21105/joss.03021}
+}
+
+@article{shannon1948mathematical,
+  title={A mathematical theory of communication},
+  author={Shannon, Claude Elwood},
+  journal={The Bell system technical journal},
+  volume={27},
+  number={3},
+  pages={379--423},
+  year={1948},
+  publisher={Nokia Bell Labs}
+}
+
+@article{pielou1966measurement,
+  title={The measurement of diversity in different types of biological collections},
+  author={Pielou, Evelyn C},
+  journal={Journal of theoretical biology},
+  volume={13},
+  pages={131--144},
+  year={1966},
+  publisher={Elsevier}
+}
+
+@article{chao2002estimating,
+  title={Estimating the number of species in a stochastic abundance model},
+  author={Chao, Anne and Bunge, John},
+  journal={Biometrics},
+  volume={58},
+  number={3},
+  pages={531--539},
+  year={2002},
+  publisher={Wiley Online Library}
+}
+
+@article{bray10jt,
+  title={JT Curtis An ordination of the upland forest communities of southern Wisconsin., 1957, 27},
+  author={Bray, JR},
+  journal={DOI: https://doi. org/10.2307/1942268},
+  pages={325--349}
+}
+
+@article{jaccard1901etude,
+  title={{\'E}tude comparative de la distribution florale dans une portion des Alpes et des Jura},
+  author={Jaccard, Paul},
+  journal={Bull Soc Vaudoise Sci Nat},
+  volume={37},
+  pages={547--579},
+  year={1901}
+}
+
+
+@article{ijms26135941,
+  AUTHOR = {Popov, Ilia V. and Manakhov, Andrey D. and Gorobets, Vladislav E. and Diakova, Kristina B. and Lukbanova, Ekaterina A. and Malinovkin, Aleksey V. and Venema, Koen and Ermakov, Alexey M. and Popov, Igor V.},
+  TITLE = {Metagenomic Investigation of Intestinal Microbiota of Insectivorous Synanthropic Bats: Densoviruses, Antibiotic Resistance Genes, and Functional Profiling of Gut Microbial Communities},
+  JOURNAL = {International Journal of Molecular Sciences},
+  VOLUME = {26},
+  YEAR = {2025},
+  NUMBER = {13},
+  ARTICLE-NUMBER = {5941},
+  URL = {https://www.mdpi.com/1422-0067/26/13/5941},
+  PubMedID = {40649719},
+  ISSN = {1422-0067},
+  ABSTRACT = {Bats serve as key ecological reservoirs of diverse microbial communities, including emerging viruses and antibiotic resistance genes. This study investigates the intestinal microbiota of two insectivorous bat species, Nyctalus noctula and Vespertilio murinus, at the Rostov Bat Rehabilitation Center in Southern Russia using whole metagenome shotgun sequencing. We analyzed taxonomic composition, functional pathways, antibiotic resistance genes, and virulence factors. Densoviruses, especially those closely related to Parus major densovirus, were the most dominant viral sequences identified. Metagenome-assembled densovirus genomes showed high sequence similarity with structural variations and clustered phylogenomically with viruses from mealworms and birds, reflecting both dietary origins and the potential for vertebrate infection. Functional profiling revealed microbial pathways associated with cell wall biosynthesis, energy metabolism, and biofilm formation. A total of 510 antibiotic resistance genes, representing 142 unique types, mainly efflux pumps and β-lactamases, were identified. Additionally, 870 virulence factor genes were detected, with a conserved set of iron acquisition systems and stress response regulators across all samples. These findings highlight the ecological complexity of bat-associated microbiota and viromes and suggest that synanthropic bats may contribute to the circulation of insect-associated viruses and antimicrobial resistance in urban settings.},
+  DOI = {10.3390/ijms26135941}
 }