Biology subjects

Maghini, D. G.

Publications and source records attributed to Maghini, D. G..

5 recordsLinked to original sources

bioRxiv2026

Habituation drives elevated antimicrobial resistance, functional, and compositional shifts in the black bear gut microbiome

Wildlife habituation across the globe poses threats to human and animal safety and alters regular ecological function, yet the wildlife, environmental, and public health ramifications are poorly characterized. The gut microbiome is a valuable proxy for these factors as it influences host health, is affected by anthropogenic exposure, and may contribute to the environmental spread of virulence factors. Despite their importance, wildlife gut microbiomes are largely uncharacterized, both in composition and function. We characterized American black bear (Ursus americanus) gut microbiomes across a spectrum of lifestyles including wild (conflict-free), habituated (conflict-prone), and captive individuals. 16S rRNA gene sequencing was used for compositional analyses and whole genome short-read sequencing (WGS) was performed on a subset of bears to investigate microbiome function and virulence factors. We found that habituated, wild, and captive bears have unique gut microbiome compositions that are indicative of their respective lifestyles. In particular, captive bears are enriched in carnivory-associated taxa and habituated bears in inflammatory taxa. WGS reveals wild bears have increased fungi and soil-associated bacteria, as well as higher proportions of unclassified reads. Habituated bears have significantly increased levels of antimicrobial resistance genes, and captive bears are enriched in enterotoxins. Our results demonstrate previously undescribed wildlife physiological and One Health consequences of habituation.

ecology↗

bioRxiv2026

Participant engagement and feedback in microbiome projects: a case of AWI-Gen 2

Returning individualized microbiome results in ways that are ethical, comprehensible, and useful remains under-explored in African settings. We nested a multi-site, mixed-methods study within the AWI-Gen Wave 2 gut microbiome sub-study of 1,801 women aged 42 - 86 years to engage the participants and provide feedback. All (1,001) participants from Agincourt and Soweto (South Africa) and Nairobi (Kenya) were invited to feedback meetings: 496 from Agincourt, 87 from Soweto, and 195 from Nairobi responded. Engagement strategies were tailored by site (small-group and home-based sessions, visual metaphors, Foldscopes, and local-language delivery). Using semi-structured discussions and structured observations analysed thematically in MAXQDA under COREQ, five cross-cutting themes emerged: (1) understanding of microbiome reports, (2) emotional responses to feedback, (3) perceived health relevance, (4) trust in research institutions, and (5) suggestions for improving engagement. Culturally grounded explanations and local-language facilitation enhanced comprehension and perceived relevance; English-heavy sessions were associated with more confusion. Most participants expressed satisfaction and described planned or enacted dietary and lifestyle changes, while frustration centred on long delays between sampling and feedback. Trust increased with transparency and individualized return of results but was often conditional on minimizing burdensome procedures such as repeat blood sampling (phlebotomy) and ensuring timely feedback. Engagement was feasible and low-cost (approximately USD 29-59 per participant) with site-specific resource needs. Limitations included constrained generalizability beyond the three study sites. Returning individualized microbiome findings in community settings in Africa is acceptable, feasible, and can motivate health-promoting behaviours when delivered promptly and in culturally and linguistically appropriate ways. IMPORTANCEMicrobiome studies rarely return individualized results in low-resource settings due to concerns about appropriate feedback and associated costs. This gap risks eroding trust and diminishing research impact. In three African communities, tailored feedback on gut microbiome profiles was provided to 778 women. By documenting a costed, multi-site engagement model and the themes influencing acceptance and actionability, this work offers a practical framework for ethically returning complex -omics results at scale in underrepresented populations - advancing scientific equity and strengthening community trust in microbiome research.

scientific communication and education↗

bioRxiv2024

Illumina Complete Long Read Assay yields contiguous bacterial genomes from human gut metagenomes

Metagenomics enables direct investigation of the gene content and potential functions of gut bacteria without isolation and culture. However, metagenome-assembled genomes are often incomplete and have low contiguity due to challenges in assembling repeated genomic elements. Long-read sequencing approaches have successfully yielded circular bacterial genomes directly from metagenomes, but these approaches are low throughput, have high DNA input requirements, and can have high error rates. Illumina has recently launched the Illumina Complete Long Read (ICLR) assay, a new approach for generating kilobase-scale reads with low DNA input requirements and high accuracy. Here, we evaluate the performance of ICLR sequencing for gut metagenomics. We sequenced a microbial mock community and ten human gut microbiome samples with standard, shotgun 2x150 paired-end sequencing, ICLR sequencing, and nanopore long-read sequencing and compared performance in read lengths, assembly contiguity, and bin quality. We find that ICLR human metagenomic assemblies have higher N50 (119.5 {+/-} 24.8 kilobases) than short read assemblies (9.9 {+/-} 4.5 kilobases; p = 0.002), and comparable N50 to nanopore assemblies (91.0 {+/-} 43.8 kilobases; p = 0.32). Additionally, we find that ICLR draft microbial genomes are more complete (94.0% {+/-} 20.6%) than nanopore draft genomes (85.9% {+/-} 23.0%; p[≤] 0.001), and that nanopore draft genomes have truncated gene lengths (924.6 {+/-} 114.7 base pairs) relative to ICLR genomes (954.6 {+/-} 71.5 base pairs; p[≤] 0.001). Overall, we find that ICLR sequencing is a promising method for high-throughput and accurate assembly of microbial genomes from gut metagenomes. ImportanceMetagenomic sequencing allows scientists to directly measure the genome content and structure of microbes residing in complex microbial communities. Traditional short-read metagenomic sequencing methods often yield fragmented genomes, whereas advanced long-read sequencing methods improve genome assembly quality but often suffer from high error rates and are logistically limited due to low throughput and high input requirements. A new method, the Illumina Complete Long Read Assay (ICLR), is capable of generating highly-accurate kilobase-scale sequencing reads with minimal input material. To evaluate the utility of ICLR in metagenomic contexts, we applied short-read, long-read, and ICLR methods to simple and complex microbial communities. We found that ICLR outperforms short-read methods, and yields comparable metagenomic assemblies to standard long-read approaches while requiring less input material. Overall, ICLR represents a high-throughput and efficient solution for assembling complete genomes from complex metagenomes.

genomics↗

bioRxiv2024

Expanding the human gut microbiome atlas of Africa

Population studies are crucial in understanding the complex interplay between the gut microbiome and geographical, lifestyle, genetic, and environmental factors. However, populations from low- and middle-income countries, which represent [~]84% of the world population, have been excluded from large-scale gut microbiome research. Here, we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,803 women from Burkina Faso, Ghana, Kenya, and South Africa. By intensively engaging with communities that range from rural and horticultural to urban informal settlements and post-industrial, we capture population diversity that represents a far greater breadth of the worlds population. Using shotgun metagenomic sequencing, we find that study site explains substantially more microbial variation than disease status. We identify taxa with strong geographic and lifestyle associations, including loss of Treponema and Cryptobacteroides species and gain of Bifidobacterium species in urban populations. We uncover a wealth of prokaryotic and viral novelty, including 1,005 new bacterial metagenome-assembled genomes, and identify phylogeography signatures in Treponema succinifaciens. Finally, we find a microbiome signature of HIV infection that is defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals to date, and paired with extensive clinical biomarkers, demographic data, and lifestyle information, provides extensive opportunity for microbiome-related discovery and research.

microbiology↗

bioRxiv2022

Achieving quantitative and accurate measurement of the human gut microbiome

Robust benchmarking studies have highlighted how measured relative microbial abundances can vary dramatically depending on how DNA is extracted, made into libraries, sequenced, and analyzed. To build upon prior research, we investigated how sample preservation and storage choices impact observed absolute microbial load and relative metagenomic and metatranscriptomic measurements. Specifically, we studied how two common stool preservatives (OMNIgene GUT OMR200 and Zymo DNA/RNA PowerShield) perform across a range of storage temperatures (-80{degrees}C, 23{degrees}C and 40{degrees}C). For immediately frozen samples with no preservatives, we observed a mean colonic load of [~]100 trillion (1.2 x 1014) prokaryotes across ten donors, revising the gut prokaryote:human cell ratio of [~]1:1 to [~]4:1. We found that both preservatives introduce significant bias in the metagenomics results; and, while OMNIgene results were robust to storage temperature, samples stored in Zymo preservative had further bias with increasing storage temperatures. In terms of measured composition, we observed a [~]1.9x and [~]1.5x difference in the metagenomic Bacteroidetes:Firmicutes ratio in OMNIgene and Zymo preservatives, respectively. Absolute abundance measurements revealed that these differences are driven by higher measured Bacteroidetes in OMNIgene-preserved samples and lower measured Firmicutes in Zymo-preserved samples. For metatranscriptomic measurements, we also found that both preservatives introduced bias, but that RNA likely degraded in samples stored in OMNIgene preservative at high temperature. In summary, we recommend the OMNIgene preservative for studies that include significant field components. For metatranscriptomics studies, we recommend kits rated for RNA preservation such as the Zymo kit; however, existing samples collected in non-RNA rated kits might also be viable for limited metatranscriptomic studies. This study demonstrates how sample collection and storage choices can affect measured microbiome research outcomes, makes additional concrete suggestions for sample handling best practices, and demonstrates the importance of including absolute abundance measurements in microbiome studies.

microbiology↗