Microbiome epidemiology in large population cohorts

My current work leverages population‑scale multi-omics data that includes a microbial component and is matched linking to electronic health records (EHR) and national registries, to associate the human microbiome with prevalent and incident human health. In a recent study focusing on a Finnish cohort (FINRISK 2002), we found that gut antibiotic‑resistance was driven by socio‑demographics and diet factors and associated with mortality and a greater risk of sepsis (Pärnänen et al., 2025). In another study involving 15,131 adults from Sweden, we demonstrated that antibiotic use could have long-term effects on the gut microbiota (Baldanzi et al., 2024). We also investigated the microbiome–resistome relationship in Japanese long-term care facilities (Kitamura et al., 2024). 

1. Pärnänen K, Ruuskanen M, Sommeria-Klein G, Laitinen V, Kantanen P, Méric G, Gazolla Volpiano C, Inouye M, Knight R, Salomaa V, Havulinna AS, Niiranen T, Lahti L. (2025) Variation and prognostic potential of the gut antibiotic resistome in the FINRISK 2002 cohort. Nature Communications 16:5963 [OA, publisher, Press release from the University of Turku]

2. Baldanzi G, Larsson A, Sayols-Baixeras S, Dekkers KF, Hammar U, Nguyen D, Graells T, Ahmad S, Gazolla Volpiano C, Méric G, Järhult JD, Tängdén T, Ludvigsson JF, Lind L, Sundström J, Michaëlsson K, Ärnlöv J, Kennedy B, Orho-Melander M, Fall T. (2024) Antibiotic use in the past 8 years and gut microbiota composition. medRxiv 2024.10.14.24315441 [OA, preprint]

3. Kitamura N, Kajihara T, Gazolla Volpiano C, Naung M, Méric G, Hirabayashi A, Yano H, Yamamoto M, Yoshida F, Kobayashi T, Yamanashi S, Kawamura T, Matsunaga N, Okochi J, Sugai M, Yahara K. (2024) Exploring the effects of antimicrobial treatment on the gut and oral microbiomes and resistomes from elderly long-term care facility residents via shotgun DNA sequencing. Microbial Genomics 10(2) [OA, publisher]

Bacterial taxonomy and genomics-based reclassifications

My earlier research harnessed large comparative‑genomics datasets to refine bacterial systematics and phylogeny. Within the Rhizobiales order, I proposed several taxonomic amendments (Gazolla Volpiano et al., 2021a). We also reclassified Streptomyces thermoautotrophicus (Gazolla Volpiano et al., 2021b) and Ochrobactrum lupini (Gazolla Volpiano et al., 2019) based on genome metrics. I was invited to collaborate on data analyses for the description of Azospirillum baldaniorum (dos Santos Ferreira et al., 2020) and A. argentinense (dos Santos Ferreira et al., 2022), as well as the proposal of six novel Streptomycetaceae genera (Madhaiyan et al., 2022). I also contributed to a genome-based taxonomy of Burkholderia sensu lato to distinguish closely related species (Bach et al., 2023). 

1. Gazolla Volpiano C, Hayashi Sant’Anna F, Ambrosini A, de São José JFB, Beneduzi A, Whitman WB, de Souza EM, Lisboa BB, Vargas LK, Passaglia LMP. (2021a) Genomic metrics applied to Rhizobiales (Hyphomicrobiales): species reclassification, identification of unauthentic genomes and false type strains. Frontiers in Microbiology 12:614957 [OA, publisher]. 

2. Gazolla Volpiano C, Hayashi Sant’Anna F, da Mota FF, Sangal V, Sutcliffe I, Munusamy M, Saravanan VS, See-Too WS, Passaglia LMP, Rosado AS. (2021b) Proposal of Carbonactinosporaceae fam. nov. within the class Actinomycetia. Reclassification of Streptomyces thermoautotrophicus as Carbonactinospora thermoautotrophica gen. nov., comb. nov. Systematic and Applied Microbiology 44(4):126223 [publisher]. 

3. Gazolla Volpiano C, Hayashi Sant’Anna F, Ambrosini A, Brito Lisboa B, Kayser Vargas L, Passaglia LMP. (2019) Reclassification of Ochrobactrum lupini as a later heterotypic synonym of Ochrobactrum anthropi based on whole-genome sequence analysis. International Journal of Systematic and Evolutionary Microbiology 69(8):2312–2314 [publisher]. 

4. dos Santos Ferreira N, Hayashi Sant’Anna F, Massena Reis V, Ambrosini A, Gazolla Volpiano C, Rothballer M, Schwab S, Baura VA, Balsanelli E, Pedrosa FO, Passaglia LMP, Maltempi de Souza E, Hartmann A, Cassan F, Zilli JE. (2020) Genome-based reclassification of Azospirillum brasilense Sp245 as the type strain of Azospirillum baldaniorum sp. nov. International Journal of Systematic and Evolutionary Microbiology 70(12):6203–6212 [publisher]. 

5. dos Santos Ferreira N, Coniglio A, Puente M, Hayashi Sant’Anna F, Maroniche G, García J, Molina R, Nievas S, Gazolla Volpiano C, Ambrosini A, Passaglia LMP, Pedraza RO, Reis VM, Zilli JE, Cassan F. (2022) Genome-based reclassification of Azospirillum brasilense Az39 as the type strain of Azospirillum argentinense sp. nov. International Journal of Systematic and Evolutionary Microbiology 72:005475 [publisher]. 

6. Madhaiyan M, Saravanan VS, See-Too WS, Gazolla Volpiano C, Hayashi Sant’Anna F, da Mota FF, Sutcliffe I, Sangal V, Passaglia LMP, Rosado AS. (2022) Genomic and phylogenomic insights into the family Streptomycetaceae lead to the proposal of six novel genera. International Journal of Systematic and Evolutionary Microbiology 72(10):005570 [publisher]. 

7. Bach E, Gazolla Volpiano C, Hayashi Sant’Anna F, Passaglia LMP. (2023) Genome-based taxonomy of Burkholderia sensu lato: distinguishing closely related species. Genetics and Molecular Biology 46(3 Suppl 1):e20230122 [OA, publisher].

Plant growth-promoting bacteria studies

I participated in several other publications on the performance of plant growth-promoting bacteria. These include reviews (Ribeiro et al., 2020; Gazolla Volpiano et al., 2022, São José et al. 2024a), book chapters (Vargas et al., 2017; Gazolla Volpiano et al., 2019), and multiple research articles (de Castilho et al., 2021; Lisboa et al., 2021; São José et al., 2019, 2023a, 2023b, 2024b; Gazolla Volpiano et al., 2018). 

1. Ribeiro IDA, Gazolla Volpiano C, Vargas LK, Granada CE, Lisboa BB, Passaglia LMP. (2020) Use of mineral weathering bacteria to enhance nutrient availability in crops: a review. Frontiers in Plant Science 11:590774 [OA, publisher]. 

2. Gazolla Volpiano C, Lisboa BB, São José JFB, Beneduzi A, Granada CE, Vargas LK. (2022) Soil–plant–microbiota interactions to enhance plant growth. Revista Brasileira de Ciência do Solo 46:e0210098 [OA, publisher]. 

3. São José JFB, Du Toit B, Gazolla Volpiano C, Lisboa BB, Tiecher T, Bayer C, Beneduzi A, Vargas LK. (2024) Soil nutrient dynamics, harvest residue management and soil organic matter conservation for the sustainability of black wattle production systems in subtropical soils: a review. New Forests 55 (2024) [publisher]. 

4. Vargas LK, Gazolla Volpiano C, Lisboa BB, Giongo A, Beneduzi A, Passaglia LMP. (2017) Potential of rhizobia as plant growth-promoting rhizobacteria. In: Zaidi A, Khan M, Musarrat J (eds) Microbes for Legume Improvement. Springer, Cham, pp. 153–174 [publisher]. 

5. Gazolla Volpiano C, Lisboa BB, Granada CE, São José JFB, de Oliveira AMR, Beneduzi A, Perevalova Y, Passaglia LMP, Vargas LK. (2019) Rhizobia for biological control of plant diseases. In: Kumar V, Prasad R, Kumar M, Choudhary D (eds) Microbiome in Plant Health and Disease. Springer, Singapore, pp. 315–336 [publisher]. 

6. de Castilho CL, Gazolla Volpiano C, Ambrosini A, Zulpo L, Passaglia LMP, Beneduzi A, de Sá ELS. (2021) Growth-promoting effects of Bradyrhizobium soybean symbionts in black oats, white oats, and ryegrass. Brazilian Journal of Microbiology 52:1451–1460 [OA, publisher].

7. Lisboa BB, Schmidt TM, Thomé AHE, Sperotto RA, Gazolla Volpiano C, São José JFB, Vargas LK, Granada CE. (2021) Indigenous rhizobial strains SEMIA 4108 and SEMIA 4107 for common bean inoculation: a biotechnological tool for cleaner and more sustainable agriculture. Experimental Agriculture 57(1):57–67 [publisher].

8. São José JFB, Gazolla Volpiano C, Vargas LK, Hernandes MAS, Lisboa BB, Schlindwein G, Sampaio JAT, Beneduzi A, Longoni LS. (2019) Influence of hot water on breaking dormancy, incubation temperature and rhizobial inoculation on germination of Acacia mearnsii seeds. Australian Forestry 82(3):157–161 [publisher]. 

9. São José JFB, Hernandes MAS, Gazolla Volpiano C, Lisboa BB, Beneduzi A, Bayer C, Simon AA, de Oliveira J, Passaglia LMP, Vargas LK. (2023) Diversity of rhizobia, symbiotic effectiveness, and potential of inoculation in Acacia mearnsii seedling production. Brazilian Journal of Microbiology 54:335–348 [publisher]. 

10. Vargas LK, São José JFB, Gazolla Volpiano C, Ambrosini A, Lisboa BB, Simon AA, de Oliveira J, Passaglia LMP, Beneduzi A. (2023) Indole acetic-producing bacteria promote the root development of Acacia mearnsii cuttings. Australian Forestry 86(3) [publisher].

11. São José JFB, Hernandes MAS, Lisboa BB, Gazolla Volpiano C, Schlindwein G, Sampaio JAT, Beneduzi A, Longoni LS. (2024) Seed size and Azospirillum brasilense Ab-V5 and Ab-V6 inoculation influences germination and early seedling vigor of Acacia mearnsii. Ciência Florestal 34(4) [OA, publisher]. 

12. Gazolla Volpiano C, Lisboa BB, São José JFB, de Oliveira AMR, Beneduzi A, Passaglia LMP, Vargas LK. (2018) Rhizobium strains in the biological control of the phytopathogenic fungi Sclerotium (Athelia) rolfsii on the common bean. Plant and Soil 432:229–243 [publisher].