Biology subjects

Ghotbi, M.

Publications and source records attributed to Ghotbi, M..

7 recordsLinked to original sources

bioRxiv2025

Effects of environmental setting and diet on the gut microbial ecology of eastern hellbenders (Cryptobranchus alleganiensis alleganiensis)

BackgroundEastern hellbenders (Cryptobranchus alleganiensis alleganiensis) have undergone substantial population declines throughout their range, leading them to become the focus of increased conservation efforts, including care in zoo and university settings. However, effective implementation of such conservation strategies often relies on a comprehensive understanding of host health, which can be directly influenced by the gut microbiome, yet characterization of gut microbiota often remains overlooked in ex situ conservation facilities. Additionally, effects on the gut microbiome associated with releasing zoo-reared animals into the wild are poorly understood. Therefore, these circumstances make hellbenders an ideal species to examine the relationship between zoo management strategies and gut microbial dynamics. Methods16S rRNA sequencing was used to investigate dissimilarities between the gut microbiome of hellbenders in zoo and wild settings and to evaluate the impact of implementing a wild diet in zoo-reared hellbenders. Additionally, the bacterial composition of zoo-released individuals and wild resident hellbenders was compared to examine the response of the gut microbiome upon release into natural habitat. Selected samples were also chosen for ITS1 rDNA sequencing as a preliminary investigation of the hellbender gut mycobiome. ResultsHuman rearing strongly affected the gut microbiome, leading to reduced bacterial richness as well as differing community structure than wild hellbenders. However, implementation of a wild diet in a zoo setting modulated the microbiome and appeared to be mainly driven by bacterial turnover. Additionally, both bacterial and fungal gut assemblages demonstrated the capacity for restructuring upon release into native habitat to become more reflective of a wild-type microbiome. ConclusionsWe completed the first study elucidating the gut microbial composition patterns of hellbenders, across both zoo and wild settings. These results provide an understanding of the potential impacts of conservation populations in zoos on gut microbial communities and also inform headstart programs of the transition of the gut microbiome post-reintroduction to the wild.

microbiology↗

bioRxiv2025

Skin lipid chemistry influences host-microbiome-pathogen interactions in snake fungal disease (ophidiomycosis)

Within host-microbiome-pathogen systems, the host chemical microenvironment is often overlooked despite its inherent role in host physiology. We used a multifaceted experimental approach encompassing culture-dependent and independent methods, metagenomic and genomic data, and deep neural network modeling to assess the impact of host skin lipid chemistry and the bacterial microbiome on the growth of Ophidiomyces ophidiicola (ophidiomycosis, snake fungal disease). Results suggest that host skin lipid chemistry (e.g., oleic acid, squalene) and bacteria isolated from wild snake skins (e.g., Chryseobacterium sp. and Stenotrophomonas maltophilia) suppress O. ophidiicola growth. Notably, the O. ophidiicola genome contains biosynthetic gene clusters (BGCs) that encode metabolites that may suppress host lipid production, facilitating fungal pathogenicity. The contrastive deep neural network produced a near-perfect alignment of snake skin lipid and microbiome profiles for both individual snakes and disease states. BGCs from bacterial genomes isolated from snake skin overlap with metagenome profiles from wild snakes and correlate with disease state. We highlight antifungal activity found in the diverse lipid milieu of snake skin and bacterial-fungal interactions (BFIs) that structure the skin microbiome. Our results illustrate a strong relationship among a fungal pathogen, the microbiome, and host skin lipid chemistry.

microbiology↗

bioRxiv2025

From Microscale to Microbial Insights: Validating High-Throughput Microvolume Extraction Methods (HiMEx) for Microbial Ecology

Extracting and directly amplifying DNA from small-volume, low-biomass samples would enable rapid, ultra-high-throughput analyses, facilitate studying microbial communities where large-volume sample collection is challenging. This can aid where conventional filtration-based methods miss capturing smaller microbes, or where microscale variability matters, such as the ocean. Here, we develop and validate physical and chemical-based DNA extractions from microvolumes with universal rRNA gene amplicons and metagenomic sequencing of all domains and viruses, on natural seawater and experimentally manipulated marine waters. Compared to 500-mL filter-based extraction, direct PCR of 3 L of lysed seawater samples consistently captured comparable microbial community composition and diversity, with reliable amplification and little to no contamination. Metagenomic results of 10 L of lysed microvolume samples captured high-quality assemblies, bacterial genomes, and diversity on par or better than our conventional extraction (48 vs 44 representative MAGs), and substantially more putative complete circular viral genomes (38 vs 1). Our approach enables scaling of rRNA gene sequencing and metagenomic library prep tremendously for a fraction of the cost of conventional methods and builds upon existing microvolume approaches by removing unnecessary expenses, like excess plasticware and expensive bead clean-up. The method expands opportunities for more comprehensive microbial community monitoring and controlled laboratory experiments.

molecular biology↗

bioRxiv2024

Absolute abundance unveils Basidiobolus as a cross-domain bridge indirectly bolstering gut microbiome homeostasis

The host microbiome is integral to metabolism, immune function, and resilience against pathogens. However, reliance on relative abundance (RA) to estimate host-associated microbiomes introduces compositional biases, while limited tools for absolute abundance (AA) quantification hinder broader applications. To address these challenges, we developed DspikeIn (https://github.com/mghotbi/DspikeIn), an R package paired with a versatile wet-lab methodology for AA quantification. Using RA and AA to compare core microbiome distributions across herpetofauna orders and their natural histories revealed starkly distinct results, driven by aggregate effects, including inherited compositional biases in RA and additional multifactorial influences. Focusing on two closely related Desmognathus species demonstrated that AA quantification enhanced resolution in differential abundance analyses and minimized false discovery rates (FDR) when identifying enriched taxa in their gut microbiomes. Keystone taxa identified through network associations also differed between RA and AA data. For example, Lactococcus and Cetobacterium were core members in Anura and Caudata, while Basidiobolus and Mortierella were core to Chelonia and Squamata, facilitating host adaptation to diverse environments, insights undetectable with RA data. AA-based network analysis further revealed that removing the Basidiobolus subnetwork increased negative interactions, highlighting its role in promoting gut homeostasis through cross-domain connectivity. Despite low redundancy, the Basidiobolus node exhibited high betweenness, efficiency, and degree, serving as a critical bridge linking disconnected nodes or modules and indirectly supporting microbiome stability, consistent with Burts structural hole theory. DspikeIn represents a transformative tool for microbiome research, enabling the transition from RA to AA quantification and delivering more accurate, consistent, and comparable results across studies. Graphical abstract DspikeIn cheatsheet O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/630554v1_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@150900forg.highwire.dtl.DTLVardef@21cd90org.highwire.dtl.DTLVardef@13ead1borg.highwire.dtl.DTLVardef@1d6fa84_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Greater host influence and promiscuity: How an invasive seaweed host has advantages over co-occurring natives

The surface microbiome of seaweed hosts is a multi-domain biofilm regulated by host-microbe and microbe-microbe interactions. The extent to which hosts influence these interactions, and potentially affect their resilience and invasion success, remains unclear. We experimentally tested whether hosts with invasion history exert more influence over their biofilms than native hosts. Biofilm formation on proxy surfaces adjacent to one invasive (Gracilaria vermiculophylla) and two native (Fucus serratus, Fucus vesiculosus) co-occurring hosts was monitored and compared to mature epiphytic biofilms of the same hosts. Only Gracilarias proxy biofilms were significantly different in community composition compared to control surfaces. Gracilarias proxy biofilms also showed the highest similarity to their adjacent algae sharing certain bacterial taxa that were absent in control treatments, indicating that colonization of the proxy surface was influenced by the host. Gracilaria and its proxy biofilm showed highest similarity in microbial network variables, suggesting a higher ability of the invader to influence connectivity and microbial associations within its biofilm. Meanwhile Gracilarias mature biofilm also showed higher variability in its prokaryotic composition over experiments, which was also reflected in a less robust microbial network in both Gracilaria and its proxy biofilms. This suggests that in addition to stronger influence in the invasive host, it was also more promiscuous towards potential symbionts from the environment. Ultimately, through examining microbial interactions, in line with previous research we found that host influence and promiscuity may play an important role in seaweed hosts to acclimate to different environmental condition and successfully thrive in new ecosystems.

molecular biology↗

bioRxiv2024

Seasonal cycles in a seaweed holobiont: A multiyear time series reveals repetitive microbial shifts and core taxa

Seasonality is an important natural feature that drives cyclic environmental changes. Seaweed holobionts, inhabiting shallow waters such as rocky shores and mud flats, are subject to seasonal changes in particular, but little is known on the influence of seasonality on their microbial communities. In this study, we conducted a bi-monthly, three-year time series to assess the seasonality of microbial epibiota in the seaweed holobiont Gracilaria vermiculophylla. Our results reveal pronounced seasonal shifts that are both taxonomic and functional, oscillating between late winter and early summer across consecutive years. While epibiota varied taxonomically between populations, they were functionally similar, indicating that seasonal variability drives functional changes, while spatial variability is more redundant. We also identified seasonal core microbiota that consistently (re)associated with the host at specific times, alongside a permanent core that is present year-round, independent of season or geography. These findings highlight the dynamic yet resilient nature of seaweed holobionts and demonstrate that their epibiota undergo predictable changes. Therewith, the research offers important insights into the temporal dynamics of seaweed-associated microbiota, and demonstrates that the relationship between seaweed host and its epibiota is not static, but naturally subject to an ongoing seasonal succession process.

ecology↗

bioRxiv2023

Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria

Reptiles and amphibians (herptiles) represent some of the more endangered and threatened species on the planet and numerous conservation strategies are being implemented with the goal of ensuring species recovery. Little is known, however, about the wild gut microbiome of herptiles and how it relates to the health of wild populations. Here we report results from both a broad survey of hosts and a more intensive sampling of hosts and geography of fungi and bacteria associated with herptile gut microbiomes. We demonstrate that bacterial communities sampled from frogs, lizards and salamanders are structured by the host higher level taxonomy and that the fungus Basidiobolus is a common and natural component of these wild gut microbiomes. Intensive sampling of multiple hosts across the ecoregions of Tennessee revealed that geography and host:geography interactions are strong predictors of distinct Basidiobolus OTUs present within a given host. Co-occurrence analyses of Basidiobolus and bacterial community diversity supports a correlation and interaction between Basidiobolus and bacteria, suggesting that Basidiobolus may play a role in structuring the bacterial community. We further the hypothesis that this interaction is advanced by unique specialized metabolism originating from horizontal gene transfer from bacteria to Basidiobolus, and demonstrate that Basidiobolus is capable of producing a diversity of specialized metabolites including small cyclic peptides. IMPORTANCEThis work significantly advances our understanding of interactions in herptile microbiomes; the role that fungi play as a structural and functional member of herptile gut microbiomes; and the chemical functions that structure host:microbiome phenotypes. We also provide an important observational system of how the gut microbiome represents a unique environment that selects for novel metabolic functions through horizontal gene transfer between fungi and bacteria. Such studies are needed to better understand the complexity of gut microbiomes in nature and will inform conservation strategies for threatened species of herpetofauna.

ecology↗