Biology subjects

Asaduzzaman, M.

Publications and source records attributed to Asaduzzaman, M..

7 recordsLinked to original sources

bioRxiv2026

Taxonomic and functional concordance between full-length ONT 16S and ONT shotgun metagenomics in the canine gut microbiome

Background: Full-length Oxford Nanopore Technologies (ONT) 16S rRNA sequencing provides a scalable view of microbial community composition and can support phylogeny-based functional prediction, but it is not equivalent to shotgun metagenomics. We asked which biological conclusions are preserved when the same canine fecal specimens are profiled by full-length ONT 16S and ONT whole-genome shotgun (WGS) sequencing, and how their agreement depends on analytical scale, reference representation and classifier. Methods: Ninety-seven fecal specimens from 51 dogs were profiled with both assays from the same DNA extract. Functional profiles predicted from NanoASV/NanoPredict with PICRUSt2 were compared with WGS-supported KEGG Ortholog (KO) profiles generated by Kadath. Taxonomy was benchmarked in a source-genome-matched RefSeq universe and in a host-specific DogMAG universe using minitax and Kraken2. Agreement was evaluated at whole-profile, feature-abundance, detection, between-sample structure and biological-inference scales. Age-associated transfer was assessed with dog-aware continuous mixed models, grouped signed-score analyses and paired/dog-blocked PERMANOVA. Results: Functional whole-profile concordance was high: median within-sample CLR Spearman correlations ranged from 0.781 to 0.860 across developmental strata, while between-sample functional structure remained significant by Mantel (rho=0.543) and Procrustes (r=0.693; both p=0.001). Feature-wise transfer was substantially weaker (median KO-wise CLR Spearman=0.318). Continuous age-associated KO slopes showed substantial cross-assay concordance (Spearman=0.727; signed-score Spearman=0.753; direction agreement=77.9%), although 1,290/5,258 eligible KOs retained significant assay-by-age interactions. Taxonomically, exact genus/species abundance agreement was much lower than agreement in between-sample ecological structure. Host-specific DogMAG improved species-level median Spearman from 0.261 to 0.656 for minitax SpeciesEstimate and from 0.181 to 0.512 for Kraken2. The classifier effect was independent of reference choice: under both RefSeq and DogMAG, minitax yielded stronger 16S-WGS concordance than Kraken2, with all eight prespecified RefSeq paired genus/species endpoints and all 10 DogMAG primary paired endpoints significant after BH correction. The same ordering extended to developmental inference, with DogMAG genus/species age-slope concordance of 0.795/0.799 for SpeciesEstimate versus 0.693/0.702 for Kraken2. Taxonomic Aitchison PERMANOVA detected age-associated structure in every assay/reference/classifier/rank combination, whereas age-by-assay interactions were consistently significant but small (R2 approximately 1.1 to 2.2%). Stricter NanoASV identity thresholds removed substantial 16S abundance without improving species-level agreement. Conclusions: The extent of cross-assay agreement depends on the level of analysis. Full-length ONT 16S preserves broad functional organization, ecological structure and much of the direction of age-associated change, but exact fine-rank composition, individual-feature abundance and effect magnitude remain assay dependent. Host-specific reference representation substantially narrows the taxonomic gap, and classifier choice exerts an additional independent effect: within the same matched reference set, minitax consistently yields stronger 16S-WGS concordance than Kraken2 across abundance, detection, ecological-distance and developmental-inference endpoints. Full-length ONT 16S is therefore well suited to broad ecological screening and hypothesis generation, whereas WGS remains preferable when conclusions depend on quantitative fine-rank composition, directly supported gene content or precise feature-level effect estimates.

microbiology↗

bioRxiv2026

Early-life canine gut microbiome maturation follows a shared age-diet trajectory within persistent host-specific structure

Early-life gut microbiome maturation remains poorly resolved in dogs. We analyzed 146 fecal samples from 19 Pumi puppies across four dietary stages using paired shotgun metagenomics and Oxford Nanopore full-length 16S sequencing. Bacterial communities shifted from Escherichia-rich facultative assemblages during breastfeeding to anaerobe-rich communities after the transition to solid food, with the strongest compositional change occurring during dietary diversification. Functional profiles changed most strongly at the start of complementary feeding, while viral profiles showed increasing phage richness and stage-dependent predicted phage-host associations. Despite this shared dietary trajectory, host identity explained a substantial fraction of microbiome variation and produced persistent dog-specific abundance patterns. Long-read 16S profiles recovered the main developmental signal despite platform-dependent taxonomic bias, and 16S-based functional inference captured pathway-level contrasts concordant with matched metagenomes. These results identify early-life canine gut microbiome maturation as an age-diet-associated but host-constrained ecological process involving coordinated bacterial, viral, and functional restructuring.

microbiology↗

bioRxiv2025

Longitudinal Long-Read Microbiome Profiling in a Canine Model Reveals How Age, Diet, and Birth Mode Shape Gut Community Dynamics

The gut microbiome undergoes dynamic age-related changes, shaped by diet and maternal factors. Here, we present a species-level, long-read 16S rRNA survey of the developing gut microbiome in a translational canine model, profiling 89 purebred Hungarian Pumis across early-life and reproductive stages. We collected 456 fecal samples longitudinally: 60 puppies followed from birth to 81 weeks, their mothers sampled during pregnancy and lactation, and adult controls from six kennels. We recorded detailed dietary metadata and reproductive status throughout the study. Age was the strongest determinant of alpha diversity, with a rapid increase during weaning and stabilization by six months of age. Beta diversity analyses revealed structured compositional transitions from early developmental phases to adulthood, including a shift toward more uniform, adult-like communities. Within-kennel variation was modest, consistent with shared environmental exposures. Mixed-effects models showed robust associations between specific taxa and age, diet, and kennel, while SparCC-inferred co-occurrence networks indicated increasing ecological complexity with age. We also demonstrated that the delivery mode - vaginal versus cesarean - impacted early-life microbiome composition: Lactobacillus spp. was significantly more abundant in cesarean-born puppies than in vaginally delivered littermates during the 8-10-week window. We also observed reproducible maternal microbiome shifts during pregnancy and lactation, with potential implications for vertical microbial transfer. Taken together, our results show that domestic dogs follow a reproducible, age-structured trajectory of microbial maturation that parallels human development, including delivery-mode effects and diet-responsive taxa. IMPORTANCEMicrobiome research is among the fastest-moving areas in biomedicine, driven by major global efforts to understand how microbial communities shape human health and disease. Dogs provide an ideal translational model because their gut microbiota more closely resembles that of humans than that of other studied animals; moreover, breeds show high within-breed genetic homogeneity, diets can be tightly regulated, and longitudinal sampling across the lifespan is feasible. Mapping shifts driven by diet and maternal factors - from early-life events through later life, including senior stages - is essential to leverage microbial plasticity for prevention, with implications for inflammation, metabolic disease, and neurodegeneration. Here, we advance this goal by providing a longitudinal, high-resolution dataset and demonstrating that full-length 16S rRNA sequencing is a powerful tool for resolving fine-scale patterns of gut colonization and maturation.

microbiology↗

bioRxiv2024

Phosphorylation of Zearalenone retains its toxicity

Microbial biotransformation of Zearalenone (ZEN) is a promising deactivation approach. The residual toxicity and stability of Zearalenone-14-phosphate (ZEN-14-P) and Zearalenone-16-phosphate (ZEN-16-P), two novel microbial phosphorylation products of ZEN, remain unknown. We investigated the cytotoxicity, oxidative stress, pro-inflammatory, and estrogenic activity of phosphorylated ZENs using porcine intestinal cells and uterine explants, and human endometrial cells, and traced their metabolic fate by LC-MS/MS analysis. The phosphorylated ZENs significantly decreased the viability of IPEC-J2 and Ishikawa cells. Similar to ZEN, phosphorylation products induced significant oxidative stress, activated the expression of pro-inflammatory cytokines, and demonstrated estrogenic activity through upregulation of estrogen-responsive genes, activation of alkaline phosphatase and proliferation of endometrial glands. LC-MS/MS analysis pointed that although phosphorylated ZENs are partially hydrolyzed to ZEN, their respective metabolic pathways differ. We conclude that phosphorylation might not be sufficient to detoxify ZEN, leaving its cytotoxic, pro-inflammatory and estrogenic properties intact. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=60 SRC="FIGDIR/small/605906v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@94e741org.highwire.dtl.DTLVardef@1da9d53org.highwire.dtl.DTLVardef@18ee655org.highwire.dtl.DTLVardef@b4035b_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2022

Bacterial communities associated with the surfaces of the fresh fruits sold around Dhaka Medical College and Hospital and their anti-microbial profiles

BackgroundNow-a-days, fresh fruits are popular sources of healthy diets with low energy density. Since they are consumed raw, it may act as a source of foodborne disease and a reservoir for antibiotic resistant organisms. This study aimed to determine microbial prevalence among the fruits sold outside Dhaka Medical College Hospital (DMCH) along with their antimicrobial profiles and to detect antimicrobial resistance genes among the resistant organisms. MethodsThirty-five different types of fruits were bought from around DMCH and analyzed for the presence of bacteria. Antibiotic sensitivity was done and ESBL, AmpC {beta}-lactamase, and MBL positive strains were identified by standard methods followed by PCR to detect ESBL, AmpC {beta}-lactamase, and MBL genes. FindingsTwenty seven different organisms were isolated and identified which were-Klebsiella spp (33{middle dot}33%), Citrobacter spp (29{middle dot}64%), Enterobacter spp (22{middle dot}22%), Escherichia coli (11{middle dot}11%), and Staphylococcus aureus (3{middle dot}70%). Among them 48{middle dot}15% organisms were resistant to different antibiotics. Only one organism (Citrobacter spp) produced ESBL phenotypically (7{middle dot}69%). Two (15{middle dot}38%) were positive for AmpC {beta}-lactamase and one of these (Enterobacter spp) possessed both SHV and CTX-M15A genes by PCR. Imipenem resistance was 84{middle dot}62% of the antibiotic resistant organisms, and 10 (90{middle dot}91%) were phenotypically MBL positive by CD test, DDS test, and MHT. By PCR, one Enterobacter spp had MBL encoding gene OXA-48. InterpretationFresh fruits, contaminated with pathogens, might be a source of transmission of resistant organisms and attribute to public health issues. FundingThe office of Directorate General of Health Service, Ministry of Health and Family Welfare, Bangladesh. ImportanceFruits sold around Dhaka Medical College and Hospital (DMCH) are usually consumed by patients, patients attendant and Health care worker. This investigation emphasized not only on the extent of bacterial contamination but also attempted to measure the anti-microbial profile of these organisms isolated from the fruits commonly available and readily consumed in and around DMCH.

microbiology↗

bioRxiv2020

Potential silencing of gene expression by PIWI-interacting RNAs (piRNAs) in somatic tissues in mollusk

PIWI/piRNA suppress transposon activity in animals, thereby safeguarding the genome from detrimental insertion mutagenesis. Recently, evidence revealed additional piRNA targets and functions in various animals. Although piRNAs are ubiquitously expressed in somatic tissues of the pearl oyster Pinctada fucata, their role is not well-characterized. Here, we report a PIWI/piRNA pathway, including piRNA biogenesis and piRNA-mediated gene regulation in P. fucata. A locked-nucleic-acid modified oligonucleotide (LNA-antagonist) was used to silence a single piRNA (piRNA0001) expression in P. fucata, which resulted in the differential expression of hundreds of endogenous genes. Target prediction analysis revealed that, following silencing, tens of endogenous genes were targeted by piRNA0001, including twelve up-regulated and nine down-regulated genes. Bioinformatic analyses suggested that different piRNA populations participate in the ping-pong amplification loop in a tissue-specific manner. These findings have improved our knowledge of the role of piRNA in mollusks, and provided evidence to understand the regulatory function of the PIWI/piRNA pathway on protein-coding genes outside of germline cells.

molecular biology↗

bioRxiv2018

The genetic legacy of continental scale admixture in Indian Austroasiatic speakers

Surrounded by speakers of Indo-European, Dravidian and Tibeto-Burman languages, around 11 million Munda (a branch of Austroasiatic language family) speakers live in the densely populated and genetically diverse South Asia. Their genetic makeup holds components characteristic of South Asians as well as Southeast Asians. The admixture time between these components has been previously estimated on the basis of archaeology, linguistics and uniparental markers. Using genome-wide genotype data of 102 Munda speakers and contextual data from South and Southeast Asia, we retrieved admixture dates between 2000 - 3800 years ago for different populations of Munda. The best modern proxies for the source populations for the admixture with proportions 0.78/0.22 are Lao people from Laos and Dravidian speakers from Kerala in India, while the South Asian population(s), with whom the incoming Southeast Asians intermixed, had a smaller proportion of West Eurasian component than contemporary proxies. Somewhat surprisingly Malaysian Peninsular tribes rather than the geographically closer Austroasiatic languages speakers like Vietnamese and Cambodians show highest sharing of IBD segments with the Munda. In addition, we affirmed that the grouping of the Munda speakers into North and South Munda based on linguistics is in concordance with genome-wide data.

genetics↗