Bio


I am a geneticist who works in the field of marine science and conservation. My work is aimed at reducing knowledge gaps in conservation science through scientific research, community partnerships and knowledge exchange across disciplines. Genomics research by our group aims to inform conservation policy and assist in reducing illegal wildlife trade.

Boards, Advisory Committees, Professional Organizations


  • Member, IUCN Species Monitoring Group (2023 - Present)
  • President, Society for Conservation Biology-Marine Section (2023 - Present)
  • Diversity and Inclusion Officer, Society for Conservation Biology-Marine Section (2019 - 2023)

Professional Education


  • Doctor of Philosophy, University of Utah (2015)
  • Bachelor of Science, Gujarat University (2004)
  • Master of Science, Maharaja Sayajirao University Baroda (2005)
  • Doctor of Philosophy, University of Utah, Genetics (2015)

Stanford Advisors


All Publications


  • The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge. Microbiome Doane, M. P., Morris, M. M., Papudeshi, B., Allen, L., Pande, D., Haggerty, J. M., Johri, S., Turnlund, A. C., Peterson, M., Kacev, D., Nosal, A., Ramirez, D., Hovel, K., Ledbetter, J., Alker, A., Avalos, J., Baker, K., Bhide, S., Billings, E., Byrum, S., Clemens, M., Demery, A. J., Lima, L. F., Gomez, O., Gutierrez, O., Hinton, S., Kieu, D., Kim, A., Loaiza, R., Martinez, A., McGhee, J., Nguyen, K., Parlan, S., Pham, A., Price-Waldman, R., Edwards, R. A., Dinsdale, E. A. 2020; 8 (1): 93

    Abstract

    BACKGROUND: The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The divergence time among these two fish groups is hypothesized to result in predictable variation among symbionts. Here, using shotgun metagenomics, we test if patterns of diversity in the skin surface microbiome across the two fish clades match predictions made by phylosymbiosis theory. We hypothesize (1) the skin microbiome will be host and clade-specific, (2) evolutionary difference in elasmobranch and teleost will correspond with a concomitant increase in host-microbiome dissimilarity, and (3) the skin structure of the two groups will affect the taxonomic and functional composition of the microbiomes.RESULTS: We show that the taxonomic and functional composition of the microbiomes is host-specific. Teleost fish had lower average microbiome within clade similarity compared to among clade comparison, but their composition is not different among clade in a null based model. Elasmobranch's average similarity within clade was not different than across clade and not different in a null based model of comparison. In the comparison of host distance with microbiome distance, we found that the taxonomic composition of the microbiome was related to host distance for the elasmobranchs, but not the teleost fishes. In comparison, the gene function composition was not related to the host-organism distance for elasmobranchs but was negatively correlated with host distance for teleost fishes.CONCLUSION: Our results show the patterns of phylosymbiosis are not consistent across both fish clades, with the elasmobranchs showing phylosymbiosis, while the teleost fish are not. The discrepancy may be linked to alternative processes underpinning microbiome assemblage, including possible historical host-microbiome evolution of the elasmobranchs and convergent evolution in the teleost which filter specific microbial groups. Our comparison of the microbiomes among fishes represents an investigation into the microbial relationships of the oldest divergence ofextant vertebrate hosts and reveals that microbial relationships are not consistent across evolutionary timescales. Video abstract.

    View details for DOI 10.1186/s40168-020-00840-x

    View details for PubMedID 32534596

  • The pandemic push: can COVID-19 reinvent conferences to models rooted in sustainability, equitability and inclusion? Socio Ecological Practice Niner, H. J., Johri, S., Meyer, J., Wasserman, S. N. 2020: 253–256
  • Taking Advantage of the Genomics Revolution for Monitoring and Conservation of Chondrichthyan Populations DIVERSITY-BASEL Johri, S., Doane, M. P., Allen, L., Dinsdale, E. A. 2019; 11 (4)

    View details for DOI 10.3390/d11040049

    View details for Web of Science ID 000467289800002

  • 'Genome skimming' with the MinION hand-held sequencer identifies CITES-listed shark species in India's exports market SCIENTIFIC REPORTS Johri, S., Solanki, J., Cantu, V., Fellows, S. R., Edwards, R. A., Moreno, I., Vyas, A., Dinsdale, E. A. 2019; 9: 4476

    Abstract

    Chondrichthyes - sharks, rays, skates, and chimeras, are among the most threatened and data deficient vertebrate species. Global demand for shark and ray derived products, drives unregulated and exploitative fishing practices, which are in turn facilitated by the lack of ecological data required for effective conservation of these species. Here, we describe a Next Generation Sequencing method (using the MinION, a hand-held portable sequencing device from Oxford Nanopore Technologies), and analyses pipeline for molecular ecological studies in Chondrichthyes. Using this method, the complete mitochondrial genome and nuclear intergenic and protein-coding sequences were obtained by direct sequencing of genomic DNA obtained from shark fin tissue. Recovered loci include mitochondrial barcode sequences- Cytochrome oxidase I, NADH2, 16S rRNA and 12S rRNA- and nuclear genetic loci such as 5.8S rRNA, Internal Transcribed Spacer 2, and 28S rRNA regions, which are commonly used for taxonomic identification. Other loci recovered were the nuclear protein-coding genes for antithrombin or SerpinC, Immunoglobulin lambda light chain, Preprogehrelin, selenium binding protein 1(SBP1), Interleukin-1 beta (IL-1β) and Recombination-Activating Gene 1 (RAG1). The median coverage across all genetic loci was 20x and sequence accuracy was ≥99.8% compared to reference sequences. Analyses of the nuclear ITS2 region and the mitochondrial protein-encoding loci allowed accurate taxonomic identification of the shark specimen as Carcharhinus falciformis, a CITES Appendix II species. MinION sequencing provided 1,152,211 bp of new shark genome, increasing the number of sequenced shark genomes to five. Phylogenetic analyses using both mitochondrial and nuclear loci provided evidence that Prionace glauca is nested within Carcharhinus, suggesting the need for taxonomic reassignment of P. glauca. We increased genomic information about a shark species for ecological and population genetic studies, enabled accurate identification of the shark tissue for biodiversity indexing and resolved phylogenetic relationships among multiple taxa. The method was independent of amplification bias, and adaptable for field assessments of other Chondrichthyes and wildlife species in the future.

    View details for DOI 10.1038/s41598-019-40940-9

    View details for Web of Science ID 000461151800060

    View details for PubMedID 30872700

    View details for PubMedCentralID PMC6418218

  • Emergent community architecture despite distinct diversity in the global whale shark (Rhincodon typus) epidermal microbiome. Scientific reports Doane, M. P., Reed, M. B., McKerral, J., Farias Oliveira Lima, L., Morris, M., Goodman, A. Z., Johri, S., Papudeshi, B., Dillon, T., Turnlund, A. C., Peterson, M., Mora, M., de la Parra Venegas, R., Pillans, R., Rohner, C. A., Pierce, S. J., Legaspi, C. G., Araujo, G., Ramirez-Macias, D., Edwards, R. A., Dinsdale, E. A. 2023; 13 (1): 12747

    Abstract

    Microbiomes confer beneficial physiological traits to their host, but microbial diversity is inherently variable, challenging the relationship between microbes and their contribution to host health. Here, we compare the diversity and architectural complexity of the epidermal microbiome from 74 individual whale sharks (Rhincodon typus) across five aggregations globally to determine if network properties may be more indicative of the microbiome-host relationship. On the premise that microbes are expected to exhibit biogeographic patterns globally and that distantly related microbial groups can perform similar functions, we hypothesized that microbiome co-occurrence patterns would occur independently of diversity trends and that keystone microbes would vary across locations. We found that whale shark aggregation was the most important factor in discriminating taxonomic diversity patterns. Further, microbiome network architecture was similar across all aggregations, with degree distributions matching Erdos-Renyi-type networks. The microbiome-derived networks, however, display modularity indicating a definitive microbiome structure on the epidermis of whale sharks. In addition, whale sharks hosted 35 high-quality metagenome assembled genomes (MAGs) of which 25 were present from all sample locations, termed the abundant 'core'. Two main MAG groups formed, defined here as Ecogroup 1 and 2, based on the number of genes present in metabolic pathways, suggesting there are at least two important metabolic niches within the whale shark microbiome. Therefore, while variability in microbiome diversity is high, network structure and core taxa are inherent characteristics of the epidermal microbiome in whale sharks. We suggest the host-microbiome and microbe-microbe interactions that drive the self-assembly of the microbiome help support a functionally redundant abundant core and that network characteristics should be considered when linking microbiomes with host health.

    View details for DOI 10.1038/s41598-023-39184-5

    View details for PubMedID 37550406

  • Stingray epidermal microbiomes are species-specific with local adaptations. Frontiers in microbiology Kerr, E. N., Papudeshi, B., Haggerty, M., Wild, N., Goodman, A. Z., Lima, L. F., Hesse, R. D., Skye, A., Mallawaarachchi, V., Johri, S., Parker, S., Dinsdale, E. A. 2023; 14: 1031711

    Abstract

    Marine host-associated microbiomes are affected by a combination of species-specific (e.g., host ancestry, genotype) and habitat-specific features (e.g., environmental physiochemistry and microbial biogeography). The stingray epidermis provides a gradient of characteristics from high dermal denticles coverage with low mucus to reduce dermal denticles and high levels of mucus. Here we investigate the effects of host phylogeny and habitat by comparing the epidermal microbiomes of Myliobatis californica (bat rays) with a mucus rich epidermis, and Urobatis halleri (round rays) with a mucus reduced epidermis from two locations, Los Angeles and San Diego, California (a 150km distance). We found that host microbiomes are species-specific and distinct from the water column, however composition of M. californica microbiomes showed more variability between individuals compared to U. halleri. The variability in the microbiome of M. californica caused the microbial taxa to be similar across locations, while U. halleri microbiomes were distinct across locations. Despite taxonomic differences, Shannon diversity is the same across the two locations in U. halleri microbiomes suggesting the taxonomic composition are locally adapted, but diversity is maintained by the host. Myliobatis californica and U. halleri microbiomes maintain functional similarity across Los Angeles and San Diego and each ray showed several unique functional genes. Myliobatis californica has a greater relative abundance of RNA Polymerase III-like genes in the microbiome than U. halleri, suggesting specific adaptations to a heavy mucus environment. Construction of Metagenome Assembled Genomes (MAGs) identified novel microbial species within Rhodobacteraceae, Moraxellaceae, Caulobacteraceae, Alcanivoracaceae and Gammaproteobacteria. All MAGs had a high abundance of active RNA processing genes, heavy metal, and antibiotic resistant genes, suggesting the stingray mucus supports high microbial growth rates, which may drive high levels of competition within the microbiomes increasing the antimicrobial properties of the microbes.

    View details for DOI 10.3389/fmicb.2023.1031711

    View details for PubMedID 36937279

  • What Can Professional Scientific Societies Do to Improve Diversity, Equity, and Inclusion: A Case Study of the American Elasmobranch Society FRONTIERS IN EDUCATION Shiffman, D. S., Alvarez, T., Bangley, C. W., Boyt, R., Cote, I. M., Daly-Engel, T. S., Davis, A. D., Gaskins, L. C., Graham, J., Graham, R. T., Johri, S., Macdonald, C. C., Paig-Tran, E., Roca, A. I., Schwieterman, G. D., Whitenack, L. B., Wiley, T. R., Ferry, L. A. 2022; 7
  • The Epidermal Microbiome Within an Aggregation of Leopard Sharks (Triakis semifasciata) Has Taxonomic Flexibility with Gene Functional Stability Across Three Time-points. Microbial ecology Doane, M. P., Johnson, C. J., Johri, S., Kerr, E. N., Morris, M. M., Desantiago, R., Turnlund, A. C., Goodman, A., Mora, M., Lima, L. F., Nosal, A. P., Dinsdale, E. A. 2022

    Abstract

    The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein-rich mucus that collectively, influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiome of the Triakis semifasciata (leopard shark) at three time-points collected across 4years to identify links between microbial groups and host metabolism. Our aims include (1) describing the variation of microbiome taxa over time and identifying recurrent microbiome members (present across all time-points); (2) investigating the relationship between the recurrent and flexible taxa (those which are not found consistently across time-points); (3) describing the functional compositions of the microbiome which may suggest links with the host metabolism; and (4) identifying whether metabolic processes are shared across microbial genera or are unique to specific taxa. Microbial members of the microbiome showed high similarity between all individuals (Bray-Curtis similarity index=82.7, where 0=no overlap, 100=total overlap) with the relative abundance of those members varying across sampling time-points, suggesting flexibility of taxa in the microbiome. One hundred and eighty-eight genera were identified as recurrent, including Pseudomonas, Erythrobacter, Alcanivorax, Marinobacter, and Sphingopxis being consistently abundant across time-points, while Limnobacter and Xyella exhibited switching patterns with high relative abundance in 2013, Sphingobium and Sphingomona in 2015, and Altermonas, Leeuwenhoekiella, Gramella, and Maribacter in 2017. Of the 188 genera identified as recurrent, the top 19 relatively abundant genera formed three recurrent groups. The microbiome also displayed high functional similarity between individuals (Bray-Curtis similarity index=97.6) with gene function composition remaining consistent across all time-points. These results show that while the presence of microbial genera exhibits consistency across time-points, their abundances do fluctuate. Microbial functions however remain stable across time-points; thus, we suggest the leopard shark microbiomes exhibit functional redundancy. We show coexistence of microbes hosted in elasmobranch microbiomes that encode genes involved in utilizing nitrogen, but not fixing nitrogen, degrading urea, and resistant to heavy metal.

    View details for DOI 10.1007/s00248-022-01969-y

    View details for PubMedID 35129649

  • Pathways to Justice, Equity, Diversity, and Inclusion in Marine Science and Conservation FRONTIERS IN MARINE SCIENCE Johri, S., Carnevale, M., Porter, L., Zivian, A., Kourantidou, M., Meyer, E. L., Seevers, J., Skubel, R. A. 2021; 8
  • Reducing Data Deficiencies: Preliminary Elasmobranch Fisheries Surveys in India, Identify Range Extensions and Large Proportions of Female and Juvenile Landings FRONTIERS IN MARINE SCIENCE Johri, S., Livingston, I., Tiwari, A., Solanki, J., Busch, A., Moreno, I., Fellows, S. R., Doane, M. P., Dinsdale, E. A. 2021; 8
  • The pandemic push: can COVID-19 reinvent conferences to models rooted in sustainability, equitability and inclusion? Socio-ecological practice research Niner, H. J., Johri, S., Meyer, J., Wassermann, S. N. 2020: 1-4

    Abstract

    The COVID-19 pandemic necessitates a change in conference formats for 2020. This shift offers a unique opportunity to address long-standing inequities in access and issues of sustainability associated with traditional conference formats, through testing online platforms. However, moving online is not a panacea for all of these concerns, particularly those arising from uneven distribution of access to the Internet and other technology. With conferences and events being forced to move online, this is a critical juncture to examine how online formats can be used to best effect and to reduce the inequities of in-person meetings. In this article, we highlight that a thoughtful and equitable move to online formats could vastly strengthen the global socio-ecological research community and foster cohesive and effective collaborations, with ecology and society being the ultimate beneficiaries.

    View details for DOI 10.1007/s42532-020-00059-y

    View details for PubMedID 34765878

    View details for PubMedCentralID PMC7446603

  • Mitochondrial genome of the silky sharkCarcharhinus falciformisfrom the British Indian Ocean Territory Marine Protected Area MITOCHONDRIAL DNA PART B-RESOURCES Johri, S., Chapple, T. K., Dinsdale, E. A., Robert, S., Block, B. A. 2020; 5 (3): 2416–17
  • Mitochondrial genome of the Silvertip shark, Carcharhinus albimarginatus, from the British Indian Ocean Territory MITOCHONDRIAL DNA PART B-RESOURCES Johri, S., Dunn, N., Chapple, T. K., Curnick, D., Savolainen, V., Dinsdale, E. A., Block, B. A. 2020; 5 (3): 2085–86
  • Complete mitochondrial genome of the gray reef shark, Carcharhinus amblyrhynchos (Carcharhiniformes: Carcharhinidae) MITOCHONDRIAL DNA PART B-RESOURCES Dunn, N., Johri, S., Curnick, D., Carbone, C., Dinsdale, E. A., Chapple, T. K., Block, B. A., Savolainen, V. 2020; 5 (3): 2080–82
  • Mitochondrial genome of the Smoothnose wedgefish Rhynchobatus laevis from the Western Indian Ocean MITOCHONDRIAL DNA PART B-RESOURCES Johri, S., Tiwari, A., Kerr, E. N., Dinsdale, E. A. 2020; 5 (3): 2083–84
  • Complete mitochondrial genome of the whitetip reef shark Triaenodon obesus from the British Indian Ocean Territory Marine Protected Area MITOCHONDRIAL DNA PART B-RESOURCES Johri, S., Chapple, T. K., Robert, S., Dinsdale, E. A., Block, B. A. 2020; 5 (3): 2347–49
  • Mitochondrial genome of the silky shark Carcharhinus falciformis from the British Indian Ocean Territory Marine Protected Area. Mitochondrial DNA. Part B, Resources Johri, S., Chapple, T. K., Dinsdale, E. A., Schallert, R., Block, B. A. 2020; 5 (3): 2416-2417

    Abstract

    We present the first mitochondrial genome of Carcharhinus falciformis from the Chagos Archipelago in the British Indian Ocean Territory (BIOT) Marine Protected Area (MPA). The mitochondrial genome of C. falciformis is 16,701 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region (D-loop). GC content was at 40.1%. The control region was 1063 bp in length. The complete mitogenome sequence of C. falciformis from the BIOT MPA will enable improved conservation measures of the CITES listed species through studies of species distribution, population abundance, fishing pressure and wildlife trade.

    View details for DOI 10.1080/23802359.2020.1775147

    View details for PubMedID 33457810

    View details for PubMedCentralID PMC7782099

  • Complete mitochondrial genome of the whitetip reef shark Triaenodon obesus from the British Indian Ocean Territory Marine Protected Area. Mitochondrial DNA. Part B, Resources Johri, S., Chapple, T. K., Schallert, R., Dinsdale, E. A., Block, B. A. 2020; 5 (3): 2347-2349

    Abstract

    We present the first mitochondrial genome of Trianenodon obesus from the Chagos Archipelago in the British Indian Ocean Territory (BIOT) Marine Protected Area. The mitogenome was 16,702 bp in length and consisted of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a non-coding control region (D-loop). GC content was at 38.9%. The control region was 1064 bp in length. This mitogenome for the BIOT MPA T. obesus differed from the previously published T. obesus genome by 15 bp and the differences include a 2 bp insertion and 13 single nucleotide polymorphisms distributed across the mitogenome in the BIOT MPA sequence. Whole mitogenome sequence of T. obesus from the Chagos archipelago presented here fills existing gaps in genetic information on marine species from the BIOT MPA and provides additional tools for species specific assessments as to the effectiveness of MPA management. In addition, methods presented here lay the framework for genetic studies in remote locations with limited infrastructure.

    View details for DOI 10.1080/23802359.2020.1775148

    View details for PubMedID 33457786

    View details for PubMedCentralID PMC7783066

  • Mitochondrial genome to aid species delimitation and effective conservation of the Sharpnose Guitarfish (Glaucostegus granulatus) META GENE Johri, S., Fellows, S. R., Solanki, J., Busch, A., Livingston, I., Mora, M., Tiwari, A., Cantu, V., Goodman, A., Morris, M. M., Doane, M. P., Edwards, R. A., Dinsdale, E. A. 2020; 24
  • Mitochondrial genome of the Silvertip shark, Carcharhinus albimarginatus, from the British Indian Ocean Territory. Mitochondrial DNA. Part B, Resources Johri, S., Dunn, N., Chapple, T. K., Curnick, D., Savolainen, V., Dinsdale, E. A., Block, B. A. 2020; 5 (3): 2085-2086

    Abstract

    The Chagos archipelago in the British Indian Ocean Territory (BIOT) has been lacking in detailed genetic studies of its chondrichthyan populations. Chondrichthyes in Chagos continue to be endangered through illegal fishing operations, necessitating species distribution and abundance studies to facilitate urgent monitoring and conservation of the species. Here, we present a complete mitochondrial genome of the Silvertip Shark, Carcharhinus albimarginatus sampled in the Chagos archipelago. The mitochondrial genome of C. albimarginatus was 16,706 bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, a replication origin and a D-loop region. GC content was at 38.7% and the control region was 1,065 bp in length. We expect that mitogenomes presented here will aid development of molecular assays for species distribution studies. Overall these studies will promote effective conservation of marine ecosystemes in the BIOT.

    View details for DOI 10.1080/23802359.2020.1765210

    View details for PubMedID 33457752

    View details for PubMedCentralID PMC7782225

  • Complete mitochondrial genome of the gray reef shark, Carcharhinus amblyrhynchos (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA. Part B, Resources Dunn, N., Johri, S., Curnick, D., Carbone, C., Dinsdale, E. A., Chapple, T. K., Block, B. A., Savolainen, V. 2020; 5 (3): 2080-2082

    Abstract

    We report the first mitochondrial genome sequences for the gray reef shark, Carcharhinus amblyrhynchos. Two specimens from the British Indian Ocean Territory were sequenced independently using two different next generation sequencing methods, namely short read sequencing on the Illumina HiSeq and long read sequencing on the Oxford Nanopore Technologies' MinION sequencer. The two sequences are 99.9% identical and are 16,705 base pairs (bp) and 16,706 bp in length. The mitogenome contains 22 tRNA genes, two rRNA genes, 13 protein-coding genes and two non-coding regions; the control region and the origin of light-strand replication (OL).

    View details for DOI 10.1080/23802359.2020.1765208

    View details for PubMedID 33457750

    View details for PubMedCentralID PMC7782339

  • Mitochondrial genome of the Smoothnose wedgefish Rhynchobatus laevis from the Western Indian Ocean. Mitochondrial DNA. Part B, Resources Johri, S., Tiwari, A., Kerr, E. N., Dinsdale, E. A. 2020; 5 (3): 2083-2084

    Abstract

    We present the first mitogenome sequence of the Smoothnose Wedgefish, Rhynchobatus laevis obtained through field sequencing on the MinION handheld sequencer. The mitochondrial genome of R. laevis is 16,560 bp in length and consisted of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a non-coding control region (D-loop). GC content was at 40.1%. The control region was 867 bp in length. Whole mitochondrial genome sequence of R. laevis will enable improved understanding of distribution, abundance, catch and trade rates of the Critically Endangered species.

    View details for DOI 10.1080/23802359.2020.1765209

    View details for PubMedID 33457751

    View details for PubMedCentralID PMC7782167