Biology subjects

Kamel, B.

Publications and source records attributed to Kamel, B..

5 recordsLinked to original sources

bioRxiv2026

Fungal microbial enrichment method enables fungal metagenomics directly from human clinical samples

Fungi play important roles in health and disease, but current methods such as culture, PCR, and amplicon sequencing cannot provide genome-level characterization directly from clinical samples. Although metagenomic sequencing could overcome these limitations, it remains impractical in clinical samples where fungal DNA is present at low abundance relative to human DNA. Here, we extend a recently described microbial enrichment method (MEM)(1) to fungi (fungal Microbial Enrichment Method; fMEM) and test the method in bronchoalveolar lavage (BAL) samples to demonstrate direct-from-sample fungal metagenomic analysis and metagenome-assembled genome (MAG) recovery. In BAL samples, fMEM depleted human DNA by more than 1000-fold while preserving fungal DNA within 10-fold, enabling shotgun sequencing from samples with fungal biomass as low as 10 pg fungal DNA per 200 {micro}L BAL. fMEM enabled de novo recovery of fungal MAGs from three of four sequenced BAL samples, including two near-complete MAGs (>90% BUSCO completeness) and one 82.1% complete MAG, with low BUSCO-estimated contamination ([≤]1.5%). Fungal MAGs recovered by fMEM also resolved potentially clinically-relevant genes, not fully predictable from taxonomy alone and revealed genomic content absent from currently-available same-species reference genomes. fMEM is compatible with a whole-genome amplification (including long-read sequencing workflows). Long reads from fMEM-processed samples provided high coverage (>10X) over fungal assemblies. fMEMs compatibility with long-read sequencing enables recovery of genes that would be difficult to assemble with short reads alone. fMEM may enable new insights into the role of human-associated fungi, impacting public health, clinical management, and research into complex diseases with suspected fungal roles. ImportanceFungi influence human health, infectious disease, and the microbiome, but direct genome analysis from clinical samples has remained impractical because fungal DNA is often overwhelmed by human DNA. We developed a fungal microbial enrichment method (fMEM) that enables direct-from-sample fungal metagenomic sequencing and genome recovery from bronchoalveolar lavage samples without requiring culture for genome assembly. fMEM recovers genome-level features not predicted by taxonomy or current same-species reference genomes and is compatible with long-read sequencing workflows that can recover loci missed by short-read sequencing. fMEM opens new opportunities for culture-independent fungal genomics, clinical microbiology, comparative genomics, and mechanistic studies of human-associated fungi.

bioengineering↗

bioRxiv2023

Genome assemblies and genetic maps highlight chromosome-scale macrosynteny in Atlantic acroporids

BackgroundCorals belong to the Cnidaria, an early branching phylum of metazoans. Over the course of their long evolutionary history, they have adapted to changing environments, such as rising sea levels and increasing ocean temperatures. While their history speaks to their evolutionary capacity, it is less clear how quickly they may respond to rapid changes. A critical aspect of adaptive capacity is the structure of their genome and the genetic diversity contained within. FindingsHere, we present chromosome-scale genome assemblies and genetic linkage maps of two critically endangered coral species, Acropora palmata and A. cervicornis, the two extant Atlantic acroporid corals. Genomes of both species were resolved into 14 chromosomes with comparable assembly sizes (A. palmata, 287Mb; A. cervicornis, 305Mb). Gene content, repeat content, gene collinearity and macrosynteny were largely preserved between the Atlantic acroporids but a 2.5 Mb inversion and 1.4 Mb translocation were detected between two of the chromosome pairs. Macrosynteny and gene collinearity decreased when comparing Atlantic with Pacific acroporids. Paracentric inversions of whole chromosome arms characterized A. hyacinthus, specifically. In the larger context of cnidarian evolution, the four acroporids and another scleractinian coral with chromosome-resolved genome assemblies retained six of 21 cnidarian ancestral linkage groups, while also privately sharing numerous ALG fission and fusion events compared to other distantly related cnidarians. Genetic linkage maps were built using a 30K genotyping array with 105 offspring in one family for A. palmata and 154 offspring across 16 families for A. cervicornis. The A. palmata consensus linkage map spans 1,013.42 cM and includes 2,114 informative markers. The A. cervicornis consensus map spans 927.36 cM across 4,859 markers. A. palmata and A. cervicornis exhibited similarly high sex-averaged genome-wide recombination rates (3.53 cM/Mb and 3.04 cM/Mb, respectively) relative to other animals. In our gamete-specific maps, we found pronounced sex-based differences in recombination, known as heterochiasmy, in this simultaneous hermaphrodite, with both species showing recombination rates 2-2.5X higher in eggs compared to sperm. ConclusionsThe genomic resources presented here are the first of their kind available for Atlantic coral species. These data sets revealed that adaptive capacity of endangered Atlantic corals is not limited by their recombination rates, with both species exhibiting high recombination rates and heterochiasmy. Nevertheless, the two sister species maintain high levels of macrosynteny and gene collinearity between them. The few large-scale rearrangements detected deserve further study as a potential cause of fertilization barriers between the species. Together, the assemblies and genetic maps presented here now enable genome-wide association studies and discovery of quantitative trait loci; tools that can aid in the conservation of these endangered corals.

evolutionary biology↗

bioRxiv2018

The in vivo transcriptome of Schistosoma mansoni in two prominent vector species, Biomphalaria pfeifferi and B. glabrata

BackgroundThe full scope of the genes expressed by schistosomes during intramolluscan development has yet to be characterized. Understanding the gene products deployed by larval schistosomes in their snail hosts will provide insights into their establishment, maintenance, asexual reproduction, ability to castrate their hosts, and their prolific production of human-infective cercariae. Using the Illumina platform, the intramolluscan transcriptome of Schistosoma mansoni was investigated in field-derived specimens of the prominent vector species Biomphalaria pfeifferi at 1 and 3 days post infection (d) and from snails shedding cercariae. These S. mansoni samples were derived from the same snails used in our complementary B. pfeifferi transcriptomic study. We supplemented this view with microarray analyses of S. mansoni from B. glabrata at 2d, 4d, 8d, 16d, and 32d.\n\nPrincipal FindingsTranscripts representing at least 7,740 (66%) of known S. mansoni genes were expressed during intramolluscan development, with the greatest number expressed in snails shedding cercariae. Many transcripts were constitutively expressed throughout development featuring membrane transporters, and metabolic enzymes involved in protein and nucleic acid synthesis and cell division. Several proteases and protease inhibitors were expressed at all stages, including some proteases usually associated with cercariae. Transcripts associated with G-protein coupled receptors, germ cell perpetuation, and stress responses and defense were well represented. We noted transcripts homologous to planarian anti-bacterial factors, several neural development or neuropeptide transcripts including neuropeptide Y, and receptors that may be associated with schistosome germinal cell maintenance and that could also impact host reproduction. In at least one snail the presence of larvae of another digenean species (an amphistome) was associated with repressed S. mansoni transcriptional activity.\n\nConclusions/SignificanceThis in vivo study, particularly featuring field-derived snails and schistosomes, provides a distinct view from previous studies of development of cultured intramolluscan stages from lab-maintained organisms. We found many highly represented transcripts with suspected or unknown functions, with connection to intramolluscan development yet to be elucidated.\n\nAUTHOR SUMMARYSchistosoma mansoni is one of the most important schistosome species causing the neglected tropical disease human intestinal schistosomiasis. By focusing on S. mansoni in vivo with its broadly distributed sub-Saharan African snail intermediate host, Biomphalaria pfeifferi, we uncover new insights and basic knowledge of this host-parasite relationship that are critical for understanding schistosomiasis transmission. We show that in vivo studies, particularly using field-derived specimens, provides a distinct view from the uniformed transcriptional responses traditionally seen from in vitro studies on S. mansoni and Biomphalaria snails. With the growing consensus that we need to supplement chemotherapy with other control methods, understanding how S. mansoni interacts with its obligatory snail host becomes integral for future planning of control programs. The data provided within provides specific analysis on how the schistosomes successfully protect themselves from host defenses and the necessary transcriptional responses required for its amplifying asexual proliferation that result in human-infective cercariae.

molecular biology↗

bioRxiv2018

Transcriptional responses of Biomphalaria pfeifferi and Schistosoma mansoni following exposure to niclosamide, with evidence for a synergistic effect on snails following exposure to both stressors

BackgroundSchistosomiasis is one of the worlds most common NTDs. Successful control operations often target snail vectors with the molluscicide niclosamide. Little is known about how niclosamide affects snails, including for Biomphalaria pfeifferi, the most important vector for Schistosoma mansoni in Africa. We used Illumina technology to explore how field-derived B. pfeifferi, either uninfected or harboring cercariae-producing S. mansoni sporocysts, respond to a sublethal exposure of niclosamide. This study afforded the opportunity to determine if snails respond differently to biotic or abiotic stressors, and if they reserve unique responses for when presented with both stressors in combination. We also examined how sporocysts respond when their snail host is exposed to niclosamide.\n\nPrincipal FindingsCercariae-producing sporocysts within snails exposed to niclosamide express ~68% of the genes in the S. mansoni genome, as compared to 66% expressed by intramolluscan stages of S. mansoni in snails not exposed to niclosamide. Niclosamide does not disable sporocysts nor does it seem to provoke from them distinctive responses associated with detoxifying a xenobiotic. For B. pfeifferi, niclosamide treatment alone increases expression of several features not up-regulated in infected snails including particular cytochrome p450s and heat shock proteins, glutathione-S-transferases, antimicrobial factors like LBP/BPI and protease inhibitors, and also provokes strong down regulation of proteases. Exposure of infected snails to niclosamide resulted in numerous up-regulated responses associated with apoptosis along with down-regulated ribosomal and defense functions, indicative of a distinctive, compromised state not achieved with either stimulus alone.\n\nConclusions/SignificanceThis study helps define the transcriptomic responses of an important and under-studied schistosome vector to S. mansoni sporocysts, to niclosamide, and to both in combination. It suggests the response of S. mansoni sporocysts to niclosamide is minimal and not reflective of a distinct repertoire of genes to handle xenobiotics while in the snail host. It also offers new insights for how niclosamide affects snails.\n\nAuthorS SummarySchistosomaisis control programs often employ the use of chemical molluscicides, such as niclosamide, to control the obligatory intermediate snail hosts. Despite its widespread use, we know little about how niclosamide affects snails like Biomphalaria pfeifferi, the most important vector Schistosoma mansoni in Africa. By sequencing the transcriptomes of uninfected and S. mansoni-infected B. pfeifferi exposed to niclosamide, we analyze the snails response to both biotic and abiotic stressors. We can also examine the response of S. mansoni to niclosamide exposure during intramolluscan development. Biomphalaria pfeifferi snails exposed only to niclosamide showed unique up-regulation of stress and defense-related transcripts not seen in snails infected with a biotic, like S. mansoni infection, alone. Schistosoma mansoni-infected B. pfeifferi exposed to niclosamide were clearly unable to regulate normal metabolic and detoxification processes. Cercariae-producing sporocysts within snails exposed to niclosamide are largely unaffected and continue to produce transcripts required for cercariae production.

molecular biology↗

bioRxiv2018

Persistent hotspots of Schistosoma mansoni transmission in the Kenyan waters of Lake Victoria: a search for snail-related answers beneath the waves

Following a four-year annual praziquantel treatment campaign the resulting prevalence of S. mansoni was seen to differ among individual villages along the Kenyan shore of Lake Victoria. We have investigated possible inherent differences in snail-related aspects of transmission among such 10 villages, including six persistent hotspot (PHS) villages ([≤]30% reduction in prevalence following repeated treatments) located along the west-facing shore of the lake, and four PZQ-responding (RESP) villages (>30% prevalence reduction following repeated treatment) along Winam Gulf. When taking into account all sampling sites and times and water hyacinth presence/absence, shoreline-associated B. sudanica from PHS and RESP villages did not differ in relative abundance or prevalence of S. mansoni infection. Water hyacinth intrusions were associated with increased B. sudanica abundance. The deeper water snail Biomphalaria choanomphala was significantly more abundant in the PHS villages and prevalence of S. mansoni among villages both before and after control was positively correlated with B. choanomphala abundance. Worm recoveries from sentinel mice did not differ between PHS and RESP villages, and abundance of non-schistosome trematode species was not associated with S. mansoni abundance. Biomphalaria choanomphala provides an alternative, deepwater mode of transmission that may favor greater persistence of S. mansoni in PHS villages. As we found evidence for ongoing S. mansoni transmission in all 10 villages, we conclude conditions conducive for transmission and reinfection occur ubiquitously. This argues for an integrated, basin-wide plan for schistosomiasis control to counteract rapid reinfections facilitated by large snail populations and movements of infected people around the lake.

epidemiology↗