Biology subjects

Tandon, K.

Publications and source records attributed to Tandon, K..

15 recordsLinked to original sources

bioRxiv2026

Accurate detection of metagenomic strain-level associations using average nucleotide identity with StrainSpy

Genetic variation among microbial strains of the same species can profoundly influence their phenotypes, ecological functions, and impacts on human health. Traditionally, the relative abundance of a species has been used to identify associations between the microbiome and disease. However, this approach overlooks intra-species genetic variation and is susceptible to spurious correlations arising from the compositional nature of abundance data and microbial load. Fast, k-mer-based algorithms can now accurately estimate strain-level Average Nucleotide Identity (ANI) in metagenomes. Despite its value as an orthogonal metric for strain-level analysis, methods for conducting ANI-based association studies remain limited. To address this, we developed StrainSpy, a statistical algorithm that identifies associations between containment ANI and variables of interest across a wide range of study designs, including longitudinal and multi-cohort designs. Re-analysis of a study examining gut microbiota recovery in 12 healthy adults following antibiotic exposure revealed novel strain-level associations, including a reduction in strain-level diversity despite species persistence. Applying StrainSpy to a multi-cohort analysis of 3,414 colorectal cancer metagenomes identified novel strain-level associations with colorectal cancer. However, in a separate collection of microbiome-immunotherapy studies, no individual strain was consistently associated across cohorts. Importantly, across both datasets, StrainSpy informed containment ANI-based machine learning models achieved comparable accuracy to traditional abundance-based methods. StrainSpy is publicly available as an R package github.com/gtonkinhill/strainspy.

microbiology↗

bioRxiv2026

Thriving to surviving: light wavelength modulates photoacclimation response in the siphonous green alga Derbesia

Algae require specific acclimation strategies to cope with spectral variability in shallow marine habitats. We investigated how the siphonous green alga Derbesia alters its photosynthetic and metabolic processes under white (WL), blue (BL), green (GL), red (RL), and far-red light (FL) by conducting photobiological and transcriptomic sampling over a 10-day period. Our results show two contrasting photoacclimation strategies: BL and GL promoted metabolic activity associated with growth, whereas FL and RL induced a low-light-like survival strategy characterized by reduced growth and suppression of the core metabolism. Photosynthetic acclimation across all conditions primarily occurs within the light dependent reactions. BL and GL promoted early acclimation marked by the immediate activation of light-harvesting complexes (LHCs) and a key transcriptional regulator MYB, and showed better acclimation marked by the sustained activation of ATPases, ATP transporters, and hormone-signaling components. BL induced a distinct transcriptional shift during the transition to prolonged exposure, including enhanced cyclic electron transport, and key regulators of protein synthesis, DNA replication, and transcriptional regulation. In contrast, FL, and to a lesser extent RL, triggered responses resembling low light acclimation with constrained growth, characterized by inefficient energy utilization, enlarged antenna systems, chloroplast proliferation with aggregations, and reduced growth rates. This study suggests high accumulation of core photopigments and reduction in chlorophyll a/b is an acclimatory response to FL, and consistently higher activation of core metabolic processes under WL likely indicates the evolutionary adaptation of Derbesia to shallow coastal environments where broad-spectrum light predominates. Additionally, our newly sequenced draft genome of the Derbesia strain for this study could serve as a genomic resource for future molecular photobiology research in Bryopsidales algae.

ecology↗

bioRxiv2025

Genomic prediction of symbiotic interactions between two Endozoicomonas clades and their coral host, Acropora loripes

BackgroundThe bacterial genus Endozoicomonas is a predominant member of the coral microbiome, widely recognised for its ubiquity and ability to form high-density aggregates within coral tissues. Hence, investigating its metabolic interplay with coral hosts offers critical insights into its ecological roles and contributions to coral health and resilience. ResultsUsing long- and short-read whole-genome sequencing of 11 Endozoicomonas strains from Acropora loripes, genome sizes were found to range between 5.8 and 7.1 Mbp. Phylogenomic analysis identified two distinct clades within the family Endozoicomonadaceae. Metabolic reconstruction uncovered clade-specific pathways, including the degradation of holobiont-derived carbon and lipids (e.g., galactose, starch, triacylglycerol, D-glucuronate), latter of suggest involvement of Endozoicomonas in host sex-type steroid hormone metabolism. A clade-specific type 6 Secretion System (T6SS) and predicted effector molecules were identified, potentially facilitating coral-bacterium symbiosis. Additionally, genomic analyses revealed diverse phosphorus acquisition strategies, implicating Endozoicomonas in holobiont phosphorus cycling and stress responses. ConclusionsThis study reveals clade-specific genomic signatures of Endozoicomonas supporting its mutualistic lifestyle within corals. Findings suggests possible roles in nutrient cycling, reproductive health, and stress resilience, offering novel insights into coral holobiont functioning and potential strategies for reef restoration.

genomics↗

bioRxiv2025

Metatranscriptomics sheds light on 'who is doing what' in the coral Porites lutea

Global decline of coral reefs due to climate change necessitates nature-based protection strategies for these crucial ecosystems. Developing such strategies requires a thorough understanding of the complex roles and interactions occurring within the coral holobiont. Using RNAseq, we investigated the active microbiome of healthy stony coral Porites lutea, focusing on the coral tissue, the green endolithic algal layer (Ostreobium layer), and the deeper coral skeleton. We identified distinct, metabolically active communities within these compartments and highlight substantial metabolic redundancy across carbon, nitrogen, and sulphur pathways. Our study provides first transcriptomic evidence of Ostreobiums ability to transfer fixed carbon to other holobiont members and the coral host. Additionally, we highlight critical roles of diverse coral holobiont members in nutrient cycling and maintaining homeostasis through scavenging of reactive oxygen and nitrogen species. This study provides novel molecular-level understanding of the functional roles played by diverse coral holobiont members in their respective compartments and underscores that corals harbour distinct microbiomes with wide-ranging functions.

microbiology↗

bioRxiv2023

Chlamydiae as symbionts of photosynthetic dinoflagellates

Chlamydiae are ubiquitous intracellular bacteria and infect a wide diversity of eukaryotes, including mammals. However, chlamydiae have never been reported to infect photosynthetic organisms. Here, we describe a novel chlamydial genus and species, Candidatus Algichlamydia australiensis (A. australiensis thereafter), capable of infecting the photosynthetic dinoflagellate Cladocopium sp. (originally isolated from a scleractinian coral). A. australiensis was confirmed to be intracellular by fluorescence in situ hybridization and confocal laser scanning microscopy, and temporally stable at the population level by monitoring its relative abundance across four weeks of host growth. Using a combination of short- and long-read sequencing, we recovered a high-quality (completeness 91.73% and contamination 0.27%) metagenome-assembled genome of A. australiensis. Phylogenetic analyses show that this chlamydial taxon represents a new genus and species within the Simkaniaceae family. A. australiensis possesses all the hallmark genes for chlamydiae-host interactions, including a complete type III secretion system. In addition, a type IV secretion system is encoded on a plasmid and has previously been observed for only three other chlamydial species. Twenty orthologous groups of genes are unique to A. australiensis, one of which is structurally similar to a protein known from Cyanobacteria and Archaeplastida involved in thylakoid biogenesis and maintenance, hinting at potential chlamydiae interactions with the chloroplasts of Cladocopium cells. Despite Cladocopium being itself a symbiont of cnidarians, a meta-analysis of 12,009 cnidarian 16S rRNA gene metabarcoding samples only returned five samples with A. australiensis sequences, suggesting A. australiensis does not associate with cnidarians. Our study shows that chlamydiae infect dinoflagellate symbionts of cnidarians, the first photosynthetic organism reported to harbor chlamydiae, thereby expanding the breadth of chlamydial hosts and providing a new contribution to the discussion around the role of chlamydiae in the establishment of the primary plastid.

microbiology↗

bioRxiv2023

Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches

Genome-scale metabolic models (GEMs) of microbial communities offer valuable insights into the functional capabilities of their members and facilitate the exploration of microbial interactions. These models are generated using different automated reconstruction tools, each relying on different biochemical databases that may affect the conclusions drawn from the in silico analysis. One way to address this problem is to employ a consensus reconstruction method that combines the outcomes of different reconstruction tools. Here, we conducted a comparative analysis of community models reconstructed from three automated tools, i.e. CarveMe, gapseq, and KBase, alongside a consensus approach, utilizing data from two marine bacterial communities. Our analysis revealed that these reconstruction approaches, while based on the same genomes, resulted in GEMs with varying numbers of genes and reactions as well as metabolic functionalities, attributed to the different databases employed. Further, our results indicated that the set of exchanged metabolites was more influenced by the reconstruction approach rather than the specific bacterial community investigated. This observation suggests a potential bias in predicting metabolite interactions using community GEMs. We also showed that consensus models encompassed a larger number of reactions and metabolites while concurrently reducing the presence of dead-end metabolites. Therefore, the usage of consensus models allows making full and unbiased use from aggregating genes from the different reconstructions in assessing the functional potential of metabolic communities. ImportanceOur study contributes significantly to the field of microbial community modeling through a comprehensive comparison of genome-scale metabolic models (GEMs) generated via various automated tools, including: CarveMe, gapseq, KBase, and a consensus approach. We revealed substantial structural disparities in model outcomes, primarily attributed to variations in the employed databases. A key finding underscored the substantial impact of the reconstruction approach on the set of exchanged metabolites, emphasizing the necessity for enhanced data integration strategies. The consensus models emerge as a powerful solution, exhibiting improved functional capabilities by encompassing a greater number of reactions, metabolites, and genes. This not only offers a more comprehensive representation of metabolic networks within bacterial communities but also shows promise in reducing variability for more accurate predictions of exchange metabolites. Overall, our research provides a critical framework for refining microbial community simulations, impacting fields from ecology to synthetic biology.

systems biology↗

bioRxiv2022

The bacterial microbiome of the coral skeleton algal symbiont Ostreobium shows preferential associations and signatures of phylosymbiosis

Ostreobium, the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communities associated with cultured strains of 5 Ostreobium clades using 16S rRNA sequencing. We shed light on their likely physical associations by comparative analysis of three datasets generated to capture (1) all algae associated bacteria (2) enriched tightly attached and potential intracellular bacteria and (3) bacteria in spent media. Our data showed that while some bacteria may be loosely attached, some tend to be tightly attached or potentially intracellular. Although colonised with diverse bacteria, Ostreobium preferentially associated with 34 bacterial taxa revealing a core microbiome. These bacteria include taxa known as nitrogen cyclers, polysaccharide degraders, sulphate reducers, antimicrobial compound producers, methylotrophs and vitamin B12 producers. By analysing co-occurrence networks of 16S rRNA datasets from Porites lutea and Paragoniastrea australensis skeleton samples, we show that the Ostreobium-bacterial associations present in the cultures are likely to also occur in their natural environment. Finally, our data show significant congruence between the Ostreobium phylogeny and the community composition of its tightly associated microbiome, largely due to the phylosymbiotic signal originating from the core bacterial taxa. This study offers insight into the Ostreobium microbiome and reveals preferential associations that warrant further testing from functional and evolutionary perspectives.

microbiology↗

bioRxiv2022

Endozoicomonas-chlamydiae interactions in cell-associated microbial aggregates of the coral Pocillopora acuta

Corals are associated with a variety of bacteria, which occur in the surface mucus layer, gastrovascular cavity, skeleton, and tissues. Some tissue-associated bacteria form clusters, termed cell-associated microbial aggregates (CAMAs), which are poorly studied. Here, we provide a comprehensive characterization of CAMAs in the coral Pocillopora acuta. Combining imaging techniques, laser capture microdissection, and amplicon and metagenome sequencing we show that CAMAs: (i) are located in the tentacle tips and may be intracellular; (ii) contain Endozoicomonas, Kistimonas (both Gammaproteobacteria), and Simkania (Chlamydiota) bacteria; (iii) Endozoicomonas may provide vitamins to its host and use secretion systems and/or pili for colonization and aggregation; (iv) Endozoicomonas and Simkania occur in distinct, but adjacent, CAMAs; (v) Simkania may rely on acetate and heme provided by neighboring Endozoicomonas. Our study provides detailed insight into coral endosymbionts, which will guide the assessment of their suitability for probiotic approaches to mitigate coral bleaching.

microbiology↗

bioRxiv2022

Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S co-occurrence networks

Interactions between microalgae and bacteria can directly influence the global biogeochemical cycles but the majority of such interactions remain unknown. 16S rRNA gene-based co-occurrence networks have potential to help identify microalgal-bacterial interactions. Here, we used data from 10 Earth microbiome projects to identify potential microalgal-bacterial associations in aquatic ecosystems. A high degree of clustering was observed in microalgal-bacterial modules, indicating densely connected neighbourhoods. Proteobacteria and Bacteroidetes predominantly co-occurred with microalgae and represented hubs of most modules. Our results also indicated that species-specificity may be a global characteristic of microalgal associated microbiomes. Several previously known associations were recovered from our network modules, validating that biologically meaningful results can be inferred using this approach. A range of previously unknown associations were recognised such as co-occurrences of Bacillariophyta with uncultured Planctomycetes OM190 and Deltaproteobacteria order NB1-j. Planctomycetes and Verrucomicrobia were identified as key associates of microalgae due to their frequent co-occurrences with several microalgal taxa. Despite no clear taxonomic pattern, bacterial associates appeared functionally similar across different environments. To summarise, we demonstrated the potential of 16S rRNA gene-based co-occurrence networks as a hypothesis-generating framework to guide more focused research on microalgal-bacterial associations.

ecology↗

bioRxiv2021

Microbiome restructuring: dominant coral bacterium Endozoicomonas species display differential adaptive capabilities to environmental changes

Bacteria in the coral microbiome play a crucial role in determining coral health and fitness, and the coral host often restructures its microbiome composition in response to external factors. An important but often neglected factor determining this microbiome restructuring is the capacity of microbiome members to adapt to a new environment. To address this issue, we examined how the microbiome structure of Acropora muricata corals changed over 9 months following a reciprocal transplant experiment. Using a combination of metabarcoding, genomics, and comparative genomics approaches, we found that coral colonies separated by a small distance harbored different dominant Endozoicomonas related phylotypes belonging to two different species, including a novel species, Candidatus Endozoicomonas penghunesis 4G, whose chromosome level (complete) genome was also sequenced in this study. Furthermore, the two dominant Endozoicomonas species showed varied adaptation capabilities when coral colonies were transplanted in a new environment. The differential adaptation capabilities of dominant members of the microbiome can a) provide distinct advantages to coral hosts when subjected to changing environmental conditions and b) have positive implications for future reefs.

microbiology↗

bioRxiv2021

Response of Endozoicomonas montiporae to heat stress and coral host lysates

Endozoicomonas, a core bacterial group in corals, may also be a coral symbiont. Endozoicomonas communities often decrease rapidly in corals under heat stress. However, how the bacteria respond to changes in temperature and coral host during heat stress is unknown. Here, we employed the cultivable, dominant species E. montiporae as a working organism to explore how Endozoicomonas responds to heat stress. We designed two experiments to clarify the extent to which E. montiporae is influenced by temperature and coral host. We detected differentially expressed protein (DEP) profiles in this bacterium at 31{degrees}C and 33{degrees}C compared to 25{degrees}C by tandem mass tags-based quantitative proteome analysis. Fifty DEPs, including many heat shock proteins, were detected when the temperature changed. The expression of antioxidant defense proteins and key pyruvate synthase proteins decreased, suggesting that E. montiporae were in a physiology of stress at 33{degrees}C. Furthermore, some proteins were differentially expressed because of the heat-stress-treated coral lysate specifically, suggesting that not only heat but also heat-induced host factors can affect the protein expression of the bacterium. This study provides an in-depth analysis of how the molecular mechanisms of Endozoicomonas are affected by heat stress and coral host.

microbiology↗

bioRxiv2020

Reciprocal transplant experiment in lakes with disparate trophic states show resolution dependent partial functional redundancy

Microbial communities are considered to be functionally redundant, but few studies have tested this hypothesis empirically. In this study, we performed an in situ reciprocal transplant experiment on the surface and bottom waters of two lakes with disparate trophic states and tracked changes in their microbial community and functional attributes for 6 weeks using high-throughput sequencing and functional approaches. The communities from both lakes were resistant to changes in composition after the reciprocal transplant, but their functions tended to become similar to the incubating lakes functional profiles. A significant linear positive relationship was observed between the microbial community and functional attributes, though with varying scales of similarity, suggesting partial functional redundancy. Furthermore, the entropy-based L-divergence measure quantified the scale of partial functional redundancy in the lakes surface and bottom waters. This study establishes and quantifies the scale of partial functional redundancy in the freshwater ecosystem through empirical investigation.

ecology↗

bioRxiv2019

A genomic view of coral-associated Prosthecochloris and a companion sulfate-reducing bacterium

Endolithic microbial symbionts in the coral skeleton may play a pivotal role in maintaining coral health. However, compared to aerobic microorganisms, research on the roles of endolithic anaerobic microorganisms and microbe-microbe interactions in the coral skeleton are still in their infancy. In our previous study, we showed that a group of coral-associated Prosthecochloris (CAP), a genus of anaerobic green sulfur bacteria, was dominant in the skeleton of the coral Isopora palifera. Though CAP is diverse, the 16S rRNA phylogeny presents it as a distinct clade separate from other free-living Prosthecochloris. In this study, we build on previous research and further characterize the genomic and metabolic traits of CAP by recovering two new near-complete CAP genomes--Candidatus Prosthecochloris isoporaea and Candidatus Prosthecochloris sp. N1--from coral Isopora palifera endolithic cultures. Genomic analysis revealed that these two CAP genomes have high genomic similarities compared with other Prosthecochloris and harbor several CAP-unique genes. Interestingly, different CAP species harbor various pigment synthesis and sulfur metabolism genes, indicating that individual CAPs can adapt to a diversity of coral microenvironments. A novel near-complete SRB genome--Candidatus Halodesulfovibrio lyudaonia--was also recovered from the same culture. The fact that CAP and various sulfate-reducing bacteria (SRB) co-exist in coral endolithic cultures and coral skeleton highlights the importance of SRB in the coral endolithic community. Based on functional genomic analysis of Ca. P. sp. N1 and Ca. H. lyudaonia, we also propose a syntrophic relationship between the SRB and CAP in the coral skeleton. ImportanceLittle is known about the ecological roles of endolithic microbes in the coral skeleton; one potential role is as a nutrient source for their coral hosts. Here, we identified a close ecological relationship between CAP and SRB. Recovering novel near-complete CAP and SRB genomes from endolithic cultures in this study enabled us to understand the genomic and metabolic features of anaerobic endolithic bacteria in coral skeletons. These results demonstrate that CAP members with similar functions in carbon, sulfur, and nitrogen metabolisms harbor different light-harvesting components, suggesting that CAP in the skeleton adapts to niches with different light intensities. Our study highlights the potential ecological roles of CAP and SRB in coral skeletons and paves the way for future investigations into how coral endolithic communities will respond to environmental changes.

microbiology↗

bioRxiv2019

FK506-binding protein 13 expression is upregulated in interstitial lung disease and correlated with clinical severity: a potentially protective role.

Pulmonary fibrosis is a progressive lung disease characterized by myofibroblast accumulation and excessive extracellular matrix deposition. Endoplasmic reticulum (ER) stress initiates the unfolded protein response (UPR), a cellular stress response pathway that has been implicated in both inflammatory and fibrotic processes. Here, we sought to investigate the role of the 13 kDa FK506-binding protein (FKBP13), an ER stress-inducible molecular chaperone, in various forms of pulmonary fibrosis. We first characterized the gene and protein expression of FKBP13 in lung biopsy samples from 24 patients with idiopathic pulmonary fibrosis (IPF) and 17 control subjects. FKBP13 expression was found to be elevated in the fibrotic regions of IPF lung tissues, and within this cohort, was correlated with declining forced vital capacity and dyspnea severity. FKBP13 expression was also increased in lung biopsies of patients with hypersensitivity pneumonitis, rheumatoid arthritis, and sarcoidosis-associated interstitial lung disease. We next evaluated the role of this protein using FKBP13-/- mice in a bleomycin model of pulmonary fibrosis. Animals were assessed for lung function and histopathology at different stages of lung injury including the inflammatory (Day 7), fibrotic (Day 21) and resolution (Day 50) phase. FKBP13-/- mice showed increased infiltration of inflammatory cells and cytokines at Day 7, increased lung elastance and fibrosis at Day 21, and impaired resolution of fibrosis at Day 50. These changes were associated with an increased number of cells that stained positive for TUNEL and cleaved caspase 3 in the FKBP13-/- lungs, indicating a heightened cellular sensitivity to bleomycin. Our findings suggest that FKBP13 is a potential biomarker for severity or progression of interstitial lung diseases, and that it has a biologically relevant role in protecting mice against bleomycin-induced injury, inflammation and fibrosis.

pathology↗

bioRxiv2019

Dominant coral bacterium Endozoicomonas acroporae metabolizes DMSP

Dominant coral-associated Endozoicomonas bacteria species are hypothesized to play a role in the coral-sulfur cycle by metabolizing Dimethylsulfoniopropionate (DMSP) into Dimethylsulfide (DMS); however, no sequenced genome to date harbors genes for this process. In this study, we assembled high-quality (>95% complete) genomes of strains of a recently added species Endozoicomonas acroporae (Acr-14T, Acr-1 and Acr-5) isolated from the coral Acropora muricata and performed comparative genomic analysis on genus Endozoicomonas. We identified the first DMSP CoA-transferase/lyase--a dddD gene homolog found in all E. acroporae strains--and functionally characterized bacteria capable of metabolizing DMSP into DMS via the DddD cleavage pathway using RT-qPCR and gas chromatography (GC). Furthermore, we demonstrated that E. acroporae strains can use DMSP as the sole carbon source and have genes arranged in an operon-like manner to link DMSP metabolism to the central carbon cycle. This study confirms the role of Endozoicomonas in the coral sulfur cycle.

ecology↗