Biology subjects

Hsiao, T.-H.

Publications and source records attributed to Hsiao, T.-H..

8 recordsLinked to original sources

bioRxiv2025

Multi-omics integration uncovers host-microbiota crosstalk underlying sexual differentiation in the shortfin eel Anguilla bicolor pacifica

The global decline in anguillid eel populations has intensified interest in understanding their biology for conservation and aquaculture. While host-gut microbiota interactions are well-characterized in homeotherms, these relationships remain poorly understood in poikilotherms during sexual differentiation. We examined gut microbiota dynamics across developmental stages in the shortfin eel Anguilla bicolor pacifica, which exhibits early sexual differentiation and a relatively short life cycle. Glass eels were cultivated in controlled freshwater conditions for three years, with sampling at key stages: glass eel, elver, sex-undetermined eel, and sex-determined eel. Full-length 16S rRNA gene sequencing revealed significant compositional shifts during development, with higher bacterial richness in adults versus younger eels. Early stages were dominated by Pseudomonadota, while sex-determined adults showed increased Deinococcota abundance. Network analysis identified Deinococcus, Sphingomonas, and Variovorax as key genera in sex-determined eels, with positive correlations between anti-Mullerian hormone gene expression and these taxa. We isolated 66 gut bacterial strains capable of metabolizing sex hormones under microaerobic conditions. These isolates, representing 22 genera across four phyla, demonstrated diverse metabolic capabilities from partial oxidation to complete steroid mineralization. Multiple strains achieved complete estradiol degradation as single isolates--a rare metabolic capability of environmental microorganisms. Comparative genomic analysis revealed widespread steroid-metabolizing genes, with Deinococcus species showing previously unreported hormone degradation capabilities. Our multi-omics analysis demonstrates that gut microbiota composition and function are intimately linked to eel sexual development, suggesting bidirectional host-microbe interactions influencing reproductive physiology. These findings advance understanding of host-microbiota interactions in aquatic vertebrates and provide implications for eel aquaculture and conservation.

microbiology↗

bioRxiv2024

Multi-Omics Mapping of Gut Microbiota's Role in Progesterone Metabolism

5-neurosteroids such as allopregnanolone and isopregnanolone play critical roles in neurological health and mood regulation, yet current therapeutic production faces significant limitations. We demonstrate that specific gut microbes represent a previously unrecognized source of bioavailable 5-neurosteroids that reach the central nervous system via the gut-brain axis. Through integrated metabolomic and genomic analyses of progesterone-amended fecal cultures, we identified Holdemania as a major producer of isopregnanolone via microbial steroid 5-reductase (BaiJ type 2) and 3{beta}-hydroxysteroid dehydrogenase/reductase. Phylogenetic analysis revealed that BaiJ-like sequences cluster predominantly within Firmicutes, with Holdemania species forming a distinct clade. In female C57BL/6 mice administered progesterone and H. filiformis, 5-neurosteroids including isopregnanolone predominated in gut tissues while allopregnanolone was the major hepatic neurosteroid. Critically, using stable isotope tracing with [3,4-{superscript 1}3C2]progesterone, we detected {superscript 1}3C-labeled isopregnanolone in brain tissue, providing direct evidence for gut-to-brain transport of microbiota-derived neurosteroids. High-fat diet significantly enhanced brain 5-neurosteroid accumulation. Global meta-analysis reveals reduced Holdemania abundance in PCOS patients (n = 346) compared to healthy women (n = 321). These findings identify gut microbiota as pharmacologically relevant neurosteroid producers and position H. filiformis as a promising probiotic candidate for enhancing endogenous neurosteroid production to treat mood disorders and other neuropsychiatric conditions. HighlightsO_LIHoldemania was identified as a major producer of 5-neurosteroids, particularly isopregnanolone, in the intestinal tract C_LIO_LIHoldemania 5-reductase (BaiJ type 2) belongs to a distinct phylogenetic clade compared to characterized Clostridium BaiJ (type 1) C_LIO_LI5-neurosteroids occurred predominantly in the cecum of female mice administered H. filiformis, progesterone, and high-fat diet C_LIO_LI{superscript 1}3C-labeled 5-neurosteroids were detected in brain tissue of female mice orally administered [3,4-{superscript 1}3C2]progesterone and H. filiformis, demonstrating gut-to-brain transport C_LIO_LIGut microbes such as H. filiformis represent promising probiotic candidates for enhancing 5-neurosteroid production and circulation via the gut-brain axis C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=146 HEIGHT=200 SRC="FIGDIR/small/628284v3_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1b85caaorg.highwire.dtl.DTLVardef@cbb352org.highwire.dtl.DTLVardef@169f7fcorg.highwire.dtl.DTLVardef@17c638_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Aromatase-independent estrogenesis: Wood-Ljungdahl pathway likely contributed to the emergence of estrogens in the biosphere

Androgen and estrogen, key sex hormones, were long thought to be exclusively produced by vertebrates. The O2-dependent aromatase that converts androgen to estrogen (estrogenesis) has never been identified in any prokaryotes. Here, we report the discovery of anaerobic estrogenesis in a Peptococcaceae bacterium (strain TUW77) isolated from the gut of the great blue-spotted mudskipper (Boleophthalmus pectinirostris). This strain exhibits unprecedented testosterone fermentation pathways, transforming testosterone into estrogens and androstanediol under anaerobic conditions. Physiological experiments revealed that strain TUW77 grows exclusively on testosterone, utilizing the androgenic C-19 methyl group as both the carbon source and electron donor. The genomic analysis identified three copies of a polycistronic gene cluster, abeABC (anaerobic bacterial estrogenesis), encoding components of a classic cobalamin-dependent methyltransferase system. These genes, highly expressed under testosterone-fed conditions, show up to 57% protein identity to the characterized EmtAB from denitrifying Denitratisoma spp., known for methylating estrogen into androgen (the reverse reaction). Tiered transcriptomic and proteomic analyses suggest that the removed C-19 methyl group is completely oxidized to CO2 via the oxidative Wood-Ljungdahl pathway, while the reducing equivalents (NADH) fully reduce remaining testosterone to androstanediol. Consistently, the addition of anthraquinone-2,6-disulfonate, an extracellular electron acceptor, to testosterone-fed TUW77 cultures enabled complete testosterone conversion into estrogen without androstanediol accumulation (anaerobic testosterone oxidation). This discovery of aromatase-independent estrogenesis in anaerobic bacteria suggests that the ancient Wood-Ljungdahl pathway may have contributed to the emergence of estrogens in the early biosphere. SignificanceUsing a testosterone-grown anaerobic bacterium as a model organism, we characterized this unusual anaerobic estrogenesis at the molecular level. Our findings challenge the long-held belief that estrogen production is exclusive to aromatase-containing vertebrates, expanding our understanding of steroid hormone biosynthesis across domains of life. The involvement of ancient strictly anaerobic Peptococcaceae members and the Wood-Ljungdahl pathway suggests that bacterial estrogenesis may predate O2-dependent estrogenesis in vertebrates. Furthermore, the identification of estrogen-producing bacteria in animal guts opens new avenues for potential microbiome-based hypoestrogenism therapies to supplement estrogen in menopausal or ovariectomized females, offering an innovative alternative to current hormone replacement strategies.

microbiology↗

bioRxiv2024

Clostridium innocuum, an opportunistic gut pathogen, inactivates host gut progesterone and arrests ovarian follicular development

HighlightsO_LIWe identified Clostridium innocuum as a key player in gut progesterone metabolism. C_LIO_LIProgesterone is converted into epipregnanolone with negligible progestogenic activity. C_LIO_LIWe identified the enzyme and mechanisms of microbial epipregnanolone production. C_LIO_LIC. innocuum caused decreased serum progesterone and follicular arrest in female mice. C_LIO_LIC. innocuum is a causal factor of progesterone resistance in women taking progesterone. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/585140v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@14cceaborg.highwire.dtl.DTLVardef@1946432org.highwire.dtl.DTLVardef@13e46d2org.highwire.dtl.DTLVardef@19b9a25_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG In briefChen et al. identified Clostridium innocuum as a major species involved in gut progesterone metabolism, with epipregnanolone as the main product, and elucidated the molecular mechanisms. C. innocuum inactivates gut progesterone in female mice, leading to decreased circulating progesterone levels. C. innocuum is also a causal factor of follicular arrest. Levels of progesterone, an endogenous female hormone, increase after ovulation; progesterone is crucial in the luteal phase to maintain successful pregnancy and prevent early miscarriage. Both endogenous and exogenous progesterone are recycled between the liver and gut; thus, the gut microbiota regulate host progesterone levels by inhibiting enterohepatic progesterone circulation. Our data indicated Clostridium innocuum as a major species involved in gut progesterone metabolism in women with infertility. C. innocuum converts progesterone into the neurosteroid epipregnanolone (with negligible progestogenic activity). We purified and characterized the corresponding enzyme, namely NADPH-dependent 5{beta}-dihydroprogesterone reductase, which is highly oxygen sensitive and whose corresponding genes are prevalent in C. innocuum. Moreover, C. innocuum-administered female C57BL/6 mice (aged 7 weeks) exhibited decreased serum progesterone levels ([~]35%). Clostridium-specific antibiotics (metronidazole) restored low serum progesterone levels in these mice. Furthermore, prolonged C. innocuum administration (12 weeks) arrested ovarian follicular development in female mice. Cytological and histological analyses indicated that C. innocuum may cause luteal phase insufficiency and affect menstrual regularity. Our findings suggest C. innocuum as a causal factor of progesterone resistance in women taking progesterone.

microbiology↗

bioRxiv2022

Circulating androgen regulation by androgen-catabolizing gut bacteria in male mouse gut

Abnormally high circulating androgen levels have been considered a causative factor for benign prostatic hypertrophy and prostate cancer. Recent studies suggested that gut bacteria can alter sex steroid profile of host; however, the underlying mechanisms and bacterial taxa remain elusive. Thauera sp. strain GDN1 is an unusual betaproteobacterium capable of aerobic and anaerobic androgen catabolism in environmental conditions (37{degrees}C) resembling the mammalian gut. The strain GDN1 administration to C57BL/6J mice through oral gavage profoundly affected gut bacterial community, along with an approximately 50% reduction in serum androgen level in male mice. Our RT-qPCR results revealed the differential expression of aerobic and anaerobic androgen catabolic genes in the mouse ileum (microaerobic) and caecum (anaerobic), respectively. Furthermore, androgenic ring-cleaved metabolites were detected in the mouse fecal extract. This study discovered that androgen serves as a carbon source of gut microbes and that androgen-catabolizing gut bacteria can modulate host circulating androgen levels. HighlightsO_LIThauera sp. strain GDN1 administration through oral gavage regulated mouse serum androgen levels. C_LIO_LIThe biochemical, genetic, and metabolite profile analyses revealed the occurrence of bacterial androgen catabolism in the mouse gut. C_LIO_LIAndrogen catabolism proceeds through the O2-dependent and O2-independent catabolic pathways in mouse ileum and caecum, respectively. C_LIO_LIA possibility to harness Thauera sp. strain GDN1 as a functional probiotic to treat hyperandrogenism. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/500890v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@515126org.highwire.dtl.DTLVardef@a696faorg.highwire.dtl.DTLVardef@1020beforg.highwire.dtl.DTLVardef@15da175_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefHsiao et al. found that oral administration of androgen-catabolizing Thauera species regulated mouse serum androgen level. They characterized the gut microbe-mediated androgen catabolism through genetic and biochemical analyses. Their discovery portends a possibility of harnessing androgen-catabolic gut bacteria as functional probiotics to treat hyperandrogenism.

microbiology↗

bioRxiv2021

Identification of essential β-oxidation genes and corresponding metabolites for estrogen degradation by actinobacteria

Steroidal estrogens (C18) are contaminants receiving increasing attention due to their endocrine-disrupting activities at sub-nanomolar concentrations. Although estrogens can be eliminated through photodegradation, microbial function is critical for removing estrogens from ecosystems devoid of sunlight exposure including activated sludge, soils, and aquatic sediments. Actinobacteria were found to be key estrogen degraders in manure-contaminated soils and estuarine sediments. Previously, we used the actinobacterium Rhodococcus sp. strain B50 as a model microorganism to identify two oxygenase genes, aedA and aedB, involved in the activation and subsequent cleavage of the estrogenic A-ring, respectively. However, genes responsible for the downstream degradation of estrogen A/B-rings remained completely unknown. In this study, we employed tiered comparative transcriptomics, gene disruption experiments, and mass spectrometry-based metabolite profile analysis to identify estrogen catabolic genes. We observed the up-regulation of thiolase-encoding aedF and aedK in the transcriptome of strain B50 grown with estrone. Consistently, two downstream estrogenic metabolites, 5-oxo-4-norestrogenic acid (C17) and 2,3,4-trinorestrogenic acid (C15), were accumulated in aedF- and aedK-disrupted strain B50 cultures. Disruption of fadD3 [3a-H-4(3-propanoate)-7a{beta}-methylhexahydro-1,5-indanedione (HIP)-coenzyme A ligase gene] in strain B50 resulted in apparent HIP accumulation in estrone-fed cultures, indicating the essential role of fadD3 in actinobacterial estrogen degradation. In addition, we detected a unique meta-cleavage product, 4,5-seco-estrogenic acid (C18), during actinobacterial estrogen degradation. Differentiating the estrogenic metabolite profile and degradation genes of actinobacteria and proteobacteria enables the cost-effective and time-saving identification of potential estrogen degraders in various ecosystems through liquid chromatography-mass spectrometry analysis and polymerase chain reaction-based functional assays.

microbiology↗

bioRxiv2020

Genetic and metabolite biomarkers reveal actinobacteria-mediated estrogen biodegradation in urban estuarine sediment

Steroidal estrogens are often accumulated in urban estuarine sediments worldwide at microgram per gram levels. These aromatic steroids have been classified as endocrine disruptors with an EC50 at sub-nanomolar concentrations and classified as Group 1 carcinogens by the World Health Organization. Microbial degradation is a naturally occurring mechanism that mineralizes estrogens in the biosphere; however, the corresponding genes in estrogen-degrading actinobacteria remain unidentified. In this study, we identified a gene cluster encoding several putative estrogen-degrading genes in actinobacterium Rhodococcus sp. strain B50. Among them, the oecB and oecC genes involved in estrogenic A-ring cleavage were identified through gene-disruption experiments. We also detected the accumulation of two extracellular estrogenic metabolites, including pyridinestrone acid (PEA) and 3a-H-4(3-propanoate)-7a{beta}-methylhexahydro-1,5-indanedione (HIP), in the estrone-fed strain B50 cultures. Since actinobacterial oecC and proteobacterial oecC shared less than 40% sequence identity, oecC could serve as a specific biomarker to differentiate the contribution of actinobacteria and proteobacteria in environmental estrogen degradation. Therefore, oecC and the extracellular metabolites PEA and HIP were used as biomarkers to investigate estrogen biodegradation in an urban estuarine sediment. Interestingly, our data suggested that actinobacteria, rather than alpha-proteobacteria function in sewage treatment plants, are actively degrading estrogens in the urban estuarine sediment. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/329094v1_ufig1.gif" ALT="Figure 1"> View larger version (93K): org.highwire.dtl.DTLVardef@17e1e23org.highwire.dtl.DTLVardef@ecc60borg.highwire.dtl.DTLVardef@be03d4org.highwire.dtl.DTLVardef@ed81d6_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIIsolation of an estrogen-degrading actinobacterium Rhodococcus sp. strain B50 and establishment of a strain B50 genetic manipulation system. C_LIO_LIStrain B50 exhibits a two-fold estrogen degradation rate of that of estrogen-degrading alpha-proteobacteria under the same cultivation conditions. C_LIO_LIFunctional characterization of two oxygenase genes, oecB and oecC, involved in estrogenic A-ring cleavage in actinobacteria. C_LIO_LIIdentification of two extracellular estrogenic metabolites, PEA and HIP, in the estrone-fed strain B50 cultures. C_LIO_LIDetection of actinobacterial oecC sequences as well as PEA and HIP in the estrone-spiked urban estuarine sediments. C_LI

microbiology↗

bioRxiv2019

Association Tests Using Copy Number Profile Curves (CONCUR) Enhances Power in Rare Copy Number Variant Analysis

Copy number variants (CNVs) are the gain or loss of DNA segments in the genome that can vary in dosage and length. CNVs comprise a large proportion of variation in human genomes and impact health conditions. To detect rare CNV association, kernel-based methods have been shown to be a powerful tool because their flexibility in modeling the aggregate CNV effects, their ability to capture effects from different CNV features, and their ability to accommodate effect heterogeneity. To perform a kernel association test, a CNV locus needs to be defined so that locus-specific effects can be retained during aggregation. However, CNV loci are arbitrarily defined and different locus definitions can lead to different performance depending on the underlying effect patterns. In this work, we develop a new kernel-based test called CONCUR (i.e., Copy Number profile Curve-based association test) that is free from a definition of locus and evaluates CNV-phenotype association by comparing individuals copy number profiles across the genomic regions. CONCUR is built on the proposed concepts of \"copy number profile curves\" to describe the CNV profile of an individual, and the \"common area under the curve (cAUC) kernel\" to model the multi-feature CNV effects. Compared to existing methods, CONCUR captures the effects of CNV dosage and length, accounts for the continuous nature of copy number values, and accommodates between- and within-locus etiological heterogeneities without the need to define artificial CNV loci as required in current kernel methods. In a variety of simulation settings, CONCUR shows comparable and improved power over existing approaches. Real data analyses suggest that CONCUR is well powered to detect CNV effects in gene pathways associated with phenotypes using data from the Swedish Schizophrenia Study and the Taiwan Biobank.\n\nAuthor summaryCopy number variants comprise a large proportion of variation in human genomes. Large rare CNVs, especially those disrupting genes or changing the dosages of genes, can carry relatively strong risks for neurodevelopmental and neuropsychiatric disorders. Kernel-based association methods have been developed for the analysis of rare CNVs and shown to be a valuable tool. Kernel methods model the collective effect of rare CNVs using flexible kernel functions that capture the characteristics of CNVs and measure CNV similarity of individual pairs. Typically kernels are created by summarizing similarity within an artificially defined \"CNV locus\" and then collapsing across all loci. In this work, we propose a new kernel-based test, CONCUR, that is based on the CNV location information contained in standard processing of the variants and removes the need for any arbitrarily defined CNV loci. CONCUR quantifies similarity between individual pairs as the common area under their copy number profile curves and is designed to detect CNV dosage, length and dosage-length interaction effects. In simulation studies and real data analysis, we demonstrate the ability of CONCUR test to detect CNV effects under diverse CNV architectures with power and robustness over existing methods.

bioinformatics↗