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- Bongcam Rudloff, Erik
(författare)
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Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action
- 2023
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Ingår i: Frontiers in Microbiology. - 1664-302X. ; 14
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Forskningsöversikt (refereegranskat)abstract
- The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish "gold standard" protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory 'omics' features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices.
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| 3. |
- Bongcam Rudloff, Erik
(författare)
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Comparison of common adverse neonatal outcomes among preterm and term infants at the National Referral Hospital in Tanzania: a case-control study
- 2022
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Ingår i: Ethiopian journal of pediatrics and child health. - : African Journals Online (AJOL). - 2413-2640 .- 2519-0334. ; 17, s. 93-104
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Tidskriftsartikel (refereegranskat)abstract
- Background: Neonatal period is a critical period in a child’s heath because it is associated with higher risk of adverse health outcomes. The objective of this study was to assess common adverse health outcomes and compare the risk of such outcomes between preterm and term neonates, in Tanzania. Methods: This was a case-control study involving infants admitted at Muhimbili National Hospital between August and October 2020. About 222 pairs of preterm and term infants were followed until discharge. Logistic regression was used to compare risk of health outcomes. Statistical sig-nificance was achieved at p–value < 0.05 and 95% confidence interval. Result: Preterm neonates had increased risk of mortality (OR = 7.2, 95% CI: 3.4----– 15.1), ap-nea (OR = 4.7, 95% CI: 3.4 – 15.1), respiratory distress syndrome (OR = 10.9, 95% CI: 6.1 – 19.6), necrotizing enterocolitis (OR = 5.5, 95% CI: 1.2 – 25.3), anemia (OR = 4.3, 95% CI: 2.8 – 6.6), pneumonia (OR = 2.7, 95% CI: 1.6 – 4.6) and sepsis (OR = 2.6, 95% CI: 1.7 – 3.9). No dif-ference in risk of intraventricular hemorrhage, patent ductus arteriosus and jaundice was ob-served. Conclusion: For promoting neonates' health, prevention and treatment of the higher risk adverse neonatal outcomes should be prioritized.
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- Bongcam Rudloff, Erik
(författare)
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Ebola virus disease and current therapeutic strategies: a review
- 2022
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Ingår i: Advances in Experimental Medicine and Biology. - Cham : Springer International Publishing. - 0065-2598. ; 1339, s. 131-137
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Konferensbidrag (refereegranskat)abstract
- The Ebola virus disease is a severe hemorrhagic fever that affects humans and other primates. Ebola virus, the causative agent of the disease, is transmitted to humans from wild animals and is highly contagious and aggressive with an estimated fatality rate to be around 50%. Since 1976, 11 outbreaks of Ebola virus disease have been reported in total, affecting mostly sub-Saharan Africa, while the most recent ongoing outbreak in the Democratic Republic of the Congo has more than 3000 reported cases and 72 deaths. Although an effective vaccine against Ebola virus disease has become available, no targeted treatment with proven efficacy upon infection is developed. Herein, we review the epidemiology of Ebola virus and the current situation in terms of prevention, diagnosis, and treatment of the disease.
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| 5. |
- Bongcam Rudloff, Erik
(författare)
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Factors associated with risk of preterm delivery in Tanzania: A case-control study at Muhimbili National Hospital
- 2021
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Ingår i: International Journal of Gynecology and Obstetrics. - : Wiley. - 0020-7292 .- 1879-3479. ; 154, s. 318-323
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Tidskriftsartikel (refereegranskat)abstract
- Objective To determine factors associated with risk of preterm delivery among pregnant women delivering at Muhimbili National Hospital in Tanzania.Methods A 1:1 case-control study was conducted to assess maternal sociodemographic, lifestyle, and current and previous obstetric factors associated with risk of preterm delivery. Mothers of preterm infants were regarded as cases and those of term infants were controls. Chi-square test and logistic regression were used to assess association between the factors and risk of preterm delivery.Results A total of 222 case-control pairs were studied. Maternal type of employment (P = 0.039), previous preterm delivery (P = 0.002), previous spontaneous abortion (P = 0.004), uterine scar (P < 0.001), parity (P = 0.034), number of prenatal care visits (P = 0.032), premature rupture of membranes (PROM) (P < 0.001), placenta previa (P = 0.002), bleeding during second trimester (P = 0.004), pre-eclampsia (P < 0.001), and maternal anemia (P = 0.033) were associated with risk of preterm delivery. The main risk factors associated with preterm delivery included previous preterm delivery (odds ratio [OR] 13.23, 95% confidence interval [CI] 1.72-101.95), placenta previa (OR 12.63, 95% CI 1.63-97.98), and PROM (OR 8.77, 95% CI 1.33-4.60).Conclusion Close monitoring of pregnant women who present any of the risk factors is important to prevent or reduce the risk of preterm delivery in Tanzania.
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| 6. |
- Bongcam Rudloff, Erik
(författare)
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The need for standardisation in life science research - an approach to excellence and trust
- 2020
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Ingår i: F1000Research. - : F1000 Research Ltd. - 2046-1402. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Today, academic researchers benefit from the changes driven by digital technologies and the enormous growth of knowledge and data, on globalisation, enlargement of the scientific community, and the linkage between different scientific communities and the society. To fully benefit from this development, however, information needs to be shared openly and transparently. Digitalisation plays a major role here because it permeates all areas of business, science and society and is one of the key drivers for innovation and international cooperation. To address the resulting opportunities, the EU promotes the development and use of collaborative ways to produce and share knowledge and data as early as possible in the research process, but also to appropriately secure results with the European strategy for Open Science (OS). It is now widely recognised that making research results more accessible to all societal actors contributes to more effective and efficient science; it also serves as a boost for innovation in the public and private sectors. However for research data to be findable, accessible, interoperable and reusable the use of standards is essential. At the metadata level, considerable efforts in standardisation have already been made (e.g. Data Management Plan and FAIR Principle etc.), whereas in context with the raw data these fundamental efforts are still fragmented and in some cases completely missing. The CHARME consortium, funded by the European Cooperation in Science and Technology (COST) Agency, has identified needs and gaps in the field of standardisation in the life sciences and also discussed potential hurdles for implementation of standards in current practice. Here, the authors suggest four measures in response to current challenges to ensure a high quality of life science research data and their re-usability for research and innovation.
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| 7. |
- Bongcam Rudloff, Erik
(författare)
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Transcriptional responses are oriented towards different components of the rearing environment in two Drosophila sibling species
- 2022
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 23
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Tidskriftsartikel (refereegranskat)abstract
- Background The chance to compare patterns of differential gene expression in related ecologically distinct species can be particularly fruitful to investigate the genetics of adaptation and phenotypic plasticity. In this regard, a powerful technique such as RNA-Seq applied to ecologically amenable taxa allows to address issues that are not possible in classic model species. Here, we study gene expression profiles and larval performance of the cactophilic siblings Drosophila buzzatii and D. koepferae reared in media that approximate natural conditions and evaluate both chemical and nutritional components of the diet. These closely related species are complementary in terms of host-plant use since the primary host of one is the secondary of the other. D. koepferae is mainly a columnar cactus dweller while D. buzzatii prefers Opuntia hosts. Results Our comparative study shows that D. buzzatii and D. koepferae have different transcriptional strategies to face the challenges posed by their natural resources. The former has greater transcriptional plasticity, and its response is mainly modulated by alkaloids of its secondary host, while the latter has a more canalized genetic response, and its transcriptional plasticity is associated with the cactus species. Conclusions Our study unveils a complex pleiotropic genetic landscape in both species, with functional links that relate detox responses and redox mechanisms with developmental and neurobiological processes. These results contribute to deepen our understanding of the role of host plant shifts and natural stress driving ecological specialization.
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| 8. |
- Brandt, Christian, et al.
(författare)
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Abundance Tracking by Long-Read Nanopore Sequencing of Complex Microbial Communities in Samples from 20 Different Biogas/Wastewater Plants
- 2020
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Ingår i: Applied Sciences. - : MDPI AG. - 2076-3417. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Anaerobic digestion (AD) has long been critical technology for green energy, but the majority of the microorganisms involved are unknown and are currently not cultivable, which makes abundance tracking difficult. Developments in nanopore long-read sequencing make it a promising approach for monitoring microbial communities via metagenomic sequencing. For reliable monitoring of AD via long reads, we established a robust protocol for obtaining less fragmented, high-quality DNA, while preserving bacteria and archaea composition, for a broad range of different biogas reactors. Samples from 20 different biogas/wastewater reactors were investigated, and a median of 20.5 Gb sequencing data per nanopore flow cell was retrieved for each reactor using the developed DNA isolation protocol. The nanopore sequencing data were compared against Illumina sequencing data while using different taxonomic indices for read classifications. The Genome Taxonomy Database (GTDB) index allowed sufficient characterisation of the abundance of bacteria and archaea in biogas reactors with a dramatic improvement (1.8- to 13-fold increase) in taxonomic classification compared to the RefSeq index. Both technologies performed similarly in taxonomic read classification with a slight advantage for Illumina in regard to the total proportion of classified reads. However, nanopore sequencing data revealed a higher genus richness after classification. Metagenomic read classification via nanopore provides a promising approach to monitor the abundance of taxa present in a microbial AD community as an alternative to 16S ribosomal RNA studies or Illumina Sequencing.
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| 9. |
- Gourlé, Hadrien, et al.
(författare)
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Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean
- 2021
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Coral reefs face an increased number of environmental threats from anthropomorphic climate change and pollution from agriculture, industries and sewage. Because environmental changes lead to their compositional and functional shifts, coral reef microbial communities can serve as indicators of ecosystem impacts through development of rapid and inexpensive molecular monitoring tools. Little is known about coral reef microbial communities of the Western Indian Ocean (WIO). We compared taxonomic and functional diversity of microbial communities inhabiting near-coral seawater and sediments from Kenyan reefs exposed to varying impacts of human activities. Over 19,000 species (bacterial, viral and archaeal combined) and 4,500 clusters of orthologous groups of proteins (COGs) were annotated. The coral reefs showed variations in the relative abundances of ecologically significant taxa, especially copiotrophic bacteria and coliphages, corresponding to the magnitude of the neighboring human impacts in the respective sites. Furthermore, the near-coral seawater and sediment metagenomes had an overrepresentation of COGs for functions related to adaptation to diverse environments. Malindi and Mombasa marine parks, the coral reef sites closest to densely populated settlements were significantly enriched with genes for functions suggestive of mitigation of environment perturbations including the capacity to reduce intracellular levels of environmental contaminants and repair of DNA damage. Our study is the first metagenomic assessment of WIO coral reef microbial diversity which provides a much-needed baseline for the region, and points to a potential area for future research toward establishing indicators of environmental perturbations.
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| 10. |
- Jhamat, Naveed, et al.
(författare)
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LPS-treatment of bovine endometrial epithelial cells causes differential DNA methylation of genes associated with inflammation and endometrial function
- 2020
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 21
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundLipopolysaccharide (LPS) endotoxin stimulates pro-inflammatory pathways and is a key player in the pathological mechanisms involved in the development of endometritis. This study aimed to investigate LPS-induced DNA methylation changes in bovine endometrial epithelial cells (bEECs), which may affect endometrial function. Following in vitro culture, bEECs from three cows were either untreated (0) or exposed to 2 and 8 mu g/mL LPS for 24h.ResultsDNA samples extracted at 0h and 24h were sequenced using reduced representation bisulfite sequencing (RRBS). When comparing DNA methylation results at 24h to time 0h, a larger proportion of hypomethylated regions were identified in the LPS-treated groups, whereas the trend was opposite in controls. When comparing LPS groups to controls at 24h, a total of 1291 differentially methylated regions (DMRs) were identified (55% hypomethylated and 45% hypermethylated). Integration of DNA methylation data obtained here with our previously published gene expression data obtained from the same samples showed a negative correlation (r=-0.41 for gene promoter, r=-0.22 for gene body regions, p<0.05). Differential methylation analysis revealed that effects of LPS treatment were associated with methylation changes for genes involved in regulation of immune and inflammatory responses, cell adhesion, and external stimuli. Gene ontology and pathway analyses showed that most of the differentially methylated genes (DMGs) were associated with cell proliferation and apoptotic processes; and pathways such as calcium-, oxytocin- and MAPK-signaling pathways with recognized roles in innate immunity. Several DMGs were related to systemic inflammation and tissue re-modelling including HDAC4, IRAK1, AKT1, MAP3K6, Wnt7A and ADAMTS17.ConclusionsThe present results show that LPS altered the DNA methylation patterns of bovine endometrial epithelial cells. This information, combined with our previously reported changes in gene expression related to endometrial function, confirm that LPS activates pro-inflammatory mechanisms leading to perturbed immune balance and cell adhesion processes in the endometrium.
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