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Microbiology and Biotechnology Letters

Review(총설)

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Environmental Microbiology (EM)  |  Microbial Genomes and Metagenomics

Microbiol. Biotechnol. Lett. 2024; 52(4): 358-371

https://doi.org/10.48022/mbl.2407.07005

Received: July 8, 2024; Revised: September 28, 2024; Accepted: October 15, 2024

Unravelling Metagenomic Studies’ Potential in Improving the Economy of Africa through Agriculture and Health

Daniel S. Agyirifo* and Jackline A. Tepson

Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana

Correspondence to :
Daniel S. Agyirifo, dagyirifo@ucc.edu.gh

Abstract

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Metagenomics, the thorough examination of a complete microbial community's genetic makeup, has become a cutting-edge discipline with profound effects on the sustainable development of Africa. This review explores metagenomic research roles in advancing important fields of health and agriculture, and their impact on the global economy. Metagenomic research helps identify beneficial microbes in agriculture that improve crop yield, soil fertility, and lessen the use of chemicals. In Africa, this knowledge supports environmental sustainability and food security. Metagenomics presents novel approaches to personalized medicine development, drug discovery, and the detection and tracking of infectious diseases. However, challenges such as inadequate finances, lack of research infrastructure, and skills in genomic and bioinformatics research hinder the fulfilment of these advantages. These challenges can be addressed through strategic investments, cooperative collaborations, and the creation of moral frameworks to guarantee the responsible and fair application of metagenomics in Africa. Through the use of metagenomic research ideas, African nations can open up new channels for economic diversification and involvement in the global bio-economy. The development of value-added goods, biofuels, and other biotechnological applications can result from the discovery of novel microbial resources and biomolecules, which will help create a more equitable and sustainable global economy.

Keywords: Metagenomics, next-generation sequencing, microbiome, agriculture, health

Graphical Abstract


Introduction

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Microbes play a significant role and have a profound impact on the environment. The ubiquitous nature of microorganisms makes them adapt to different environments such as the soil, water, air, plants, and animals’ surfaces and guts of various animals. Various microorganisms and their economic importance have been studied through culture techniques and expression assays. However, since microorganisms interact with other microbes in their community, current research focuses on simultaneously studying microorganisms and how they interact with their environment. Culture methods over the years have been successful in microbial studies, however, several studies have established that not all microorganisms are culturable even though they play an important role in the microbial community [1, 2]. This has necessitated the use of advanced modified methods and advanced sequencing technologies. The scientific field of metagenomics integrates genetics, ecology, and technology to reveal this previously unexplored area [3, 4]. By directly assessing genetic material extracted from environmental samples, it overcomes the constraints of conventional genetic investigations such as phenotypic complexity, technological limitations, genetic interactions, epigenetic factors, and evolutionary dynamics. Metagenomics is the study of the collective genomes of microorganisms found in a specific environment or sample. It involves the direct extraction and study of the genetic material from ambient samples without isolating and cultivating individual microbial species [5].

According to [6], this method of studying microorganisms without a culture makes it feasible to examine the complete range of microbes, including those that are hard or impossible to cultivate artificially. Research in metagenomics has accelerated with the introduction of next-generation sequencing (NGS) technologies. Rapid and cost-effective analysis of microbial communities has been made possible through the use of high-throughput sequencing platforms, such as Illumina, PacBio and Oxford Nanopore [7]. In addition, to handle and interpret large amounts of metagenomic data, bioinformatics tools and databases have advanced. Tools like QIIME, Galaxy, MG-RAST, MetaPhIAn, and Kraken have become crucial in analyzing microbial diversity, composition, and functional potential. As sequencing technologies advanced, especially with the advent of next-generation sequencing technologies, metagenomic research grew to encompass the examination of complete microbial genomes and their functional capacities [8]. The advent of next-generation sequencing (NGS) technology in the late 2000s, transformed metagenomic research. This allowed for the unprecedented depth and size of sequencing entire microbial communities [9]. This has opened up new possibilities for addressing critical global challenges in agriculture and health, particularly in regions like Africa, where issues such as food security, disease management, and sustainable development are of paramount importance.

This review explores the transformative potential of metagenomics in advancing key sectors such as agriculture and health, with a focus on its implications for sustainable development in Africa. By examining the applications of metagenomics in improving crop yields, enhancing soil health, managing diseases, and understanding the human microbiome, this paper aims to highlight the significant contributions of this cutting-edge research to the continent's economic and social development. Moreover, it discusses the challenges and prospects associated with implementing metagenomic studies in Africa, emphasizing the need for strategic investments and collaborations to fully realize the potential of this technology.

Methodology

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This review was conducted through a comprehensive search of the published literature on the applications and potential of metagenomics research, with a focus on its impact on agriculture, health, and the economy.

Literature search strategy

A systematic search of academic databases, including PubMed, Google Scholar, and Web of Science, was conducted to identify relevant studies. Keywords such as “metagenomics,” “next-generation sequencing,” “microbiome,” “agriculture,” “health,” “Africa,” and “sustainable development” were used, both individually and in combination, to retrieve articles, reviews, and reports that address the topics of interest. The initial search yielded over 300 potentially relevant articles. These were screened based on title and abstract to identify studies that specifically discussed the use of metagenomics in the context of Africa and other countries and its implications for sustainable development. Articles were included if they:

1. Presented original research, systematic reviews, or meta-analyses on metagenomics applications in African agriculture, health, or the economy.

2. Discussed the challenges, opportunities, and prospects of metagenomics research in Africa.

3. Provided insights into how metagenomics can contribute to addressing key development goals in Africa.

After the initial screening, 90 articles were selected for full-text review. The reference lists of these articles were also examined to identify any additional relevant studies.

Data extraction and synthesis of findings

For each selected study, key information was extracted, including, the background and context of metagenomics research in Africa, the methodologies used in the study (e.g., next-generation sequencing platforms, bioinformatics tools), the findings and conclusions drawn by the authors, the geographical focus of the study, particularly any relevance to Africa, potential economic impacts of metagenomics research, including diversification, value-addition, and biotechnology development, challenges and barriers to implementing metagenomics research in Africa, and proposed strategies and recommendations for leveraging metagenomics to drive sustainable development in Africa.

Results and Discussion

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Development of the era of metagenomic studies

In the conventional sequencing approach, DNA is extracted from a culture of genetically identical cells. Nevertheless, preliminary metagenomic research has demonstrated that there are probably sizable populations of microbes in diverse settings that are not cultivable, making them impossible to sequence [2]. The idea of metagenomics first surfaced in the late 1990s building on developments in DNA sequencing technology and bioinformatics [10]. These have been applied in several African countries with South Africa leading this new horizon (Fig. 1).

Figure 1.A map of Africa showing countries where metagenome research is active. The deep shaded colour indicates the countries with high volume metagenomic research activities.

Clone-based techniques were the mainstay of early efforts in the field. Environmental samples' DNA was cloned into plasmids or bacterial artificial chromosomes (BACs), after which it was sequenced. The number of clones that could be examined and the size of the inserts were the only constraints on this method, which revealed details about the phylogenetic and functional diversity of microbial communities [11]. The study of 16S ribosomal RNA (rRNA) gene sequences was the main focus of early metagenomic research, and it offered insights into the taxonomic diversity of microbial communities [12]. The 16S rRNA amplicon sequencing involves amplifying and sequencing a specific region of the 16S ribosomal RNA gene, which is present in all bacteria and archaea. This approach allows researchers to identify the taxonomic composition of a microbial community, including the presence and relative abundance of different bacterial and archaeal taxa. The data obtained from 16S rRNA amplicon sequencing can be used to assess the diversity of a microbial community, including measures of alpha diversity (within-sample diversity) and beta diversity (between-sample diversity). Some studies done using 16S rRNA amplicon research include evaluating the gut microbiome composition in individuals with different health conditions, such as inflammatory bowel disease, obesity, or diabetes, and assessing the impact of dietary interventions or probiotic supplementation on the gut microbiome [13, 14], and characterizing the microbial communities associated with soil environments, such as the rhizosphere, marine sediments, or the built environment [15].

Shotgun metagenomics, or whole-genome sequencing, is a more comprehensive approach to studying microbial communities. Instead of targeting a specific region or gene as the 16S rRNA amplicon, this method targets the entire genomic content of a sample, providing more complete information about the microbial community. Shot-gun metagenomics can provide insights into the functional capabilities of a microbial community by identifying the genes and metabolic pathways present [16]. It further includes detecting and characterizing individual microbial strains within a community, providing a more detailed understanding of the diversity and dynamics [17]. Shotgun sequencing data can also be used to track the prevalence and distribution of antibiotic-resistant genes within a microbial community [18]. Some research done using shotgun sequencing includes; investigating the functional potential of the gut microbiome in individuals with Crohn's disease or type 2 diabetes [19], exploring the microbiome of extreme environments, such as deep-sea hydrothermal vents or high-altitude soils, to discover novel microbial diversity and metabolic capabilities [20].

Understanding complex microbial communities

Understanding the makeup, variety, and possible uses of intricate microbial communities, metagenomics has fundamentally changed our knowledge of the microbiological world [21]. Through the metagenomics approach, researchers have discovered a great deal of previously unidentified or uncultured microbial species, as well as the enormous and yet undiscovered diversity of microorganisms found in diverse habitats, [22]. Furthermore, metagenomics has enabled researchers to understand the metabolic capacities and functional functions of microbes in their native environments by examining the collective genomes of microbial communities. This has given researchers insights into the processes at the eco-system level that these bacteria mediate. Numerous novel genes, proteins, and enzymes with potential biotechnological and industrial applications, including drug discovery, bioremediation, and biofuel generation, have been identified through metagenomic techniques [23, 24]. The study of intricate microbial interactions within communities, such as symbiotic partnerships, competitive dynamics, and metabolic interdependencies, has also been made possible by metagenomics. Moreover, metagenomics has significantly contributed to the investigation of the human microbiome, offering new perspectives on the function of microbial communities in health, illness, and the emergence of many ailments [25].

Understanding the role of microorganisms in global biochemical cycles, such as the carbon, nitrogen, and sulfur cycles, is crucial for understanding the impact of microbial communities on Earth's climate and developing strategies to mitigate climate change. Metagenomics has revealed the dissemination of antibiotic-resistance genes among microbial communities, which is crucial for combating the rise of antibiotic-resistant bacteria and their impact on public health [26]. The analysis of extremophile microbes and their adaptations to hostile conditions, which can influence the search for extraterrestrial life and help understand the limitations of life on Earth and beyond, is one last area in which metagenomics has implications in astrobiology [27].

The state of agriculture in africa and the challenges observed

Agriculture practice in Africa is confronted by many issues that mitigate the region's food security and sustainable development. Compared to industrialized countries, agricultural yields in Africa are substantially lower. This is mostly because of low soil fertility, restricted access to better seeds and fertilizers, and inadequate irrigation infrastructure [28]. Productivity may be increased by updating farming methods and improving agricultural inputs. Furthermore, crop productivity in Africa is seriously threatened by the increasingly unpredictable rainfall patterns and rising temperatures brought on by climate change. Extreme weather events like droughts and floods have the potential to destroy crops and negatively affect food security. This emphasizes the need to create climate-smart agricultural practices and enhance resistance to these changes [29].

Crop losses from pests and diseases continue to be a significant problem, significantly lowering agricultural output, in addition to productivity issues and climate-related concerns. The absence of contemporary agricultural technologies such as automation, irrigation systems, and post-harvest storage facilities hamper efficiency and productivity [30]. These losses might be reduced by bolstering pest and disease control techniques, such as the application of integrated pest management and disease-resistant crop types. African farmers might profit immensely from increased access to these technologies and investments in rural infrastructure. Lastly, a major issue in African agriculture is soil degradation, which includes nutrient depletion, erosion, and declining fertility. This emphasizes the necessity of putting sustainable soil management techniques into place to improve soil health and sustain long-term agricultural productivity [31].

Metagenomics in enhancing crop yield and soil health

Metagenomics presents a promising avenue for addressing the issues that African agriculture faces, namely concerning disease management, crop breeding, and soil health. Metagenomics can aid in the development of superior crop types with higher yields and resistance to pests and diseases by identifying beneficial microorganisms that support plant growth and stress resilience [32]. Furthermore, metagenomics can examine the microbial communities present in soil, detecting microorganisms that enhance soil fertility and nutrient cycling and offering insights into the microbial activities related to nutrient cycling, like phosphorus solubilization and nitrogen fixation [33]. Metagenomics has provided insights into soil microbial diversity and its impact on soil health and fertility. By analyzing soil samples, researchers can identify beneficial microbes that promote nutrient cycling, enhance soil structure, and suppress soil-borne pathogens. Understanding these microbial communities aid in developing sustainable agricultural practices, such as the use of biofertilizers and biopesticides (Table 1).

Table 1 . Metagenomics research that has impacted the economy of Africa through agriculture.

Study AreaCountryKey FindingsOutcomeReferences
Biofuel productionIndiaMetagenomics offers a novel approach to exploring uncharacterised microbial communities for enzyme discovery.Application of novel enzymes in biofuel production.
Enzymes discovered		[40]
Climate impact on agricultureAustralia and UK
Zimbabwe
Tanzania		Climate change increases pathogen incidence and severity, affecting food security.
Significant differences in microbial communities between symptomatic and non-symptomatic plants.
Microbial applications reduce reliance on chemical fertilizers and pesticides, promoting environmental health.		Integrated pest management and adaptive agricultural practices.
Insights into the role of endophytic microbiota in banana health, suggesting potential for biocontrol strategies against Fusarium wilt		[10]
[41]
[28]
[29]
[39]
Water
Microbiome		Kenya
Germany
USA
Malaysia		High levels of nitrogen and ammonia in wastewater treatment plants.
Bioplastic biofilms were distinct and enriched with sulfate-reducing microorganisms (SRM) Lagoons Identification of diverse organohalide-respiring bacteria (OHRB) in mangrove soils
Identified pathogenic zoonotic bacteria in ornamental fish.		It demonstrated the potential of aerobic denitrifying bacteria for bioremediation of nitrogenous compounds in wastewater and mangroves.
Bioplastic influences biogeochemical activities related to sulfate reduction.		[42]
[43]
[44]
[45]
Plant-Microbe interactionSouth Africa
Chile and Spain		Metagenomics captures the diversity of unculturable microorganisms.
Microbial communities significantly enhance plant growth and soil health
Chemical communication between plants and microbes leads to induced systemic resistance (ISR). Identification of various metabolites involved in signalling.
Identification of a core microbiota in Arabidopsis.
Interactions include plant species, ecotype, developmental stage, and microbial interactions.
Identification of genes involved in carbon fixation, nitrogen fixation, phosphorus solubilization, sulfur cycling, and stress resistance in the maize rhizosphere		Potential for developing eco-friendly plant protection strategies through beneficial microbes[33]
[36]
[34]
[46]
Agricultural productivity and microbial community genomesIndia
Burkina Faso		Metagenomics aids in pathogen identification, disease resistance breeding, pest control, and abiotic stress management.
Identified five new cowpea-infecting viruses in addition to three previously known.		Comprehensive understanding of metagenomics applications in agriculture, providing insights for sustainable practices.[32]
[47]
[30]
Agricultural soilsChina
United States
Switzerland
Nigeria
South Africa		Cattle, chicken, and swine manure are primary sources of antibiotics and ARGs.
Microbial interactions influence nutrient cycling and community structure.
Soil-borne pathogens cause significant crop yield losses.
Beneficial microorganisms isolated can suppress soil-borne pathogens.
Co-digestion enhanced microbial diversity and methane production.
Energy metabolism pathways of oxidative phosphorylation and methane metabolism		Management of antibiotic contamination in agricultural soils and its potential risks to human health.
Understanding aggregate-based approaches is essential for predicting microbial community functions and soil health.
Enhanced understanding of compost microbiomes can lead to improved biocontrol strategies.		[48]
[49]
[1]
[38]
[35]
[50]
[51]
[16]
Agriculture
Animals		NigeriaFirst genomic characterization of RHDV2 in Sub-Saharan Africa. One full and two partial RHDV2 genomes were identified.
High prevalence of Salmonella spp. and E. coli.		Genomic surveillance of RHDV2 to track its origin and inform public health policy[52]
[53]
Food processingArgentina
China
Ireland
Ghana
South Africa
Nigeria
Benin
Burkina Faso
Uganda
Kenya
Ethiopia		Diverse microbiota in raw milk; dominance of spoilage-associated bacteria in processing stages.
Metabolic pathways for aromatic compounds involved in flavour production were elucidated
Food pathogen surveillance		Identification of potential probiotic strains
highlighting factors affecting food safety and quality
Targeted inoculations for desired flavour development
The study provided insights into the bacterial diversity in smoked fish, which can help improve food safety and quality.		[54]
[55]
[56]
[57]
[58]


A study [33] highlighted the role of soil microbial diversity in nutrient cycling and plant productivity. The researchers used metagenomics to identify microbial genes involved in nitrogen fixation and phosphorus solubilization, demonstrating their importance in sustainable agriculture. Applying these microorganisms to maize fields resulted in yield increases of up to 30% and decreased reliance on artificial fertilizers. This discovery has important implications for agriculture in Africa, where nutrient depletion and soil degradation are major problems.

Metagenomics in plant-microbe interactions

The rhizosphere, the soil region influenced by plant roots, harbours a diverse microbial community critical for plant health. Metagenomic studies have revealed the complex interactions between plants and their associated microbiomes. These interactions can enhance plant growth, nutrient uptake, and resistance to diseases. Engineering plant-associated microbiomes through microbial inoculants or genetic modifications holds promise for improving crop yields and resilience. A land-mark study by [34] used metagenomics to characterize the rhizosphere microbiome of Arabidopsis thaliana. They identified key microbial taxa associated with plant health, highlighting their potential for developing microbial inoculants. In a different study by [35] metagenomics was used to investigate the role of beneficial microbes in suppressing plant pathogens. The research demonstrated that certain microbial communities can induce systematic resistance in plants, providing a natural defense mechanism against diseases. Researchers in Kenya also utilized metagenomics to identify the microorganisms that give maize crops resistance to heat and drought [36]. Applying these bacteria to maize plants made it possible for them to flourish in harsh environments, lowering crop losses and enhancing food security (Table 1).

Metagenomics in pest and disease management

Metagenomics plays a crucial role in identifying and managing agricultural pests and diseases. Researchers can develop targeted biocontrol strategies by analyzing the microbial communities associated with pests. A study on biocontrol strategies identified microbial communities associated with pest insects [37]. The findings helped in developing targeted biocontrol strategies using specific microbial agents to control pest populations. Additionally, metagenomics aids in detecting plant pathogens at early stages allowing for timely intervention and disease management. In another study [38], metagenomics was employed to detect early-stage infections of Phytophthora infestans in potato crops. Early detection allowed for timely intervention and reduced crop losses. Metagenomic research was also employed in Uganda to identify the causative agents of banana bacterial wilt, a catastrophic agricultural disease [39]. This realization facilitated the creation of quick diagnostic instruments and monitoring techniques, enabling farmers to quickly identify and contain the outbreak and protect their livelihoods (Table 1).

Metagenomics holds the key to revealing the genetic makeup of microbes that are advantageous to soil and crops, which might revolutionize African agriculture. The success stories presented here show how metagenomics can be used to generate biopesticides, increase crop resilience, improve soil fertility, and combat crop diseases. It is anticipated that as the sector develops further, even more creative solutions will emerge to promote food security and sustainable agricultural development throughout Africa.

Metagenomics in food processing

Food processing is the transformation of agricultural products into food, or of one form of food into another form. Food processing takes many forms, from grinding grain into raw flour, home cooking, and complex industrial methods used in the making of convenience foods. Most food processing methods play important roles in reducing waste and improving the preservation of food, thus reducing any negative impact of agriculture on the environment and improving food security. The quality, safety, and sustainability of food products have become increasingly important as the food industry continues to evolve. The application of cutting-edge technologies is crucial in achieving these goals. Metagenomics is a powerful tool that can enhance our understanding of the microbial ecosystems involved in food processing. Metagenomics offers novel insights that were previously not accessible through conventional culturing methods by providing an overview of the microbial communities present in food products and processing environments.

One major application of metagenomics in food processing is microbial profiling. Microbial profiling is a technique that allows for the identification and characterization of diverse microorganisms, including bacteria, fungi, and viruses, that inhabit the various stages of food production. In a study conducted in a diary processing plant by [56], researchers used 16S rRNA gene sequencing to profile the bacterial communities at various stages to assess the microbial diversity throughout the production chain, from raw milk to the final product. The analysis revealed distinct microbial signatures at different processing steps, allowing the identification of critical control points and the development of targeted strategies to maintain product quality and safety (Table 1).

Metagenomics also helps in the detection of pathogens in the food industry. By sequencing the genetic material from food samples, the presence of pathogenic microorganisms, even at low abundance can be identified through metagenomics. This rapid and accurate detection of potential threats to food safety enables immediate interventions, safeguarding consumer health and trust. A study conducted by [55] focused on the development and implementation of a rapid, on-site detection method for E. coli O157: H7 in a fresh produce processing facility. The researchers used a loop-mediated isothermal amplification (LAMP) assay to quickly identify the presence of the pathogen in raw materials, processing equipment, and finished products. The real-time, culture-independent approach allowed the facility to make informed decisions and implement immediate corrective actions, improving the overall food safety of its products.

The application of metagenomics also extends to the field of fermentation monitoring. Metagenomics allows for the tracking of dynamic microbial communities during the production of fermented foods. This in turn enables food producers to better control and predict the outcomes of fermentation processes, leading to more consistent and higher-quality final products. In a study by [57], the microbial communities in a cocoa bean fermentation heap were investigated using a culture-independent approach to elucidate the microbial diversity, structure, functional annotation and mapping unto metabolic pathways (Table 1). The results provided insights into the cocoa microbiome, identifying fermentation processes carried out by complex microbial communities and metabolic pathways encoding aromatic compounds that are required for flavour and aroma production. The results obtained will help producers develop targeted inoculations to produce the desired chocolate flavour or targeted metabolic pathways for the selection of microbes for good aroma and flavour compound formation.

The food industry is facing complex challenges, and the adoption of metagenomics has become increasingly important. This technology provides unprecedented insights into the world of microbes involved in food processing, enabling food manufacturers to enhance the quality, safety, and sustainability of food products. As metagenomics continues to evolve, we can expect to see even more widespread implementation of this cutting-edge approach, paving the way for a future where the science of microbial communities revolutionizes the way we produce, process, and consume our food.

Health challenges in Africa

Africa has a particularly severe infectious disease burden, accounting for a disproportionately large fraction of the worldwide burden of communicable diseases. Urbanization, dietary changes, and sedentary lifestyles, conditions like mental health disorders, diabetes, cancer, and cardiovascular disease are becoming more prevalent. Many African healthcare systems are still primarily focused on treating infectious diseases and frequently lack the resources and expertise to properly manage the rising burden of non-communicable diseases (NCDs), this epidemiological transformation presents a substantial challenge [59]. Broader environmental and socioeconomic conditions, such as poverty, lack of access to clean water and sanitation, and food insecurity, are the root causes of these various health issues. The low health outcomes seen throughout the African continent are a result of these socioeconomic determinants of health, underscoring the necessity of an all-encompassing, multi-sectoral strategy to address the intricate and interconnected health issues the continent faces.

Contribution of metagenomics to human microbiome studies

The human microbiome, comprising trillions of microbes residing in and on the human body, is vital for health and disease. Metagenomics has been instrumental in characterizing the diversity and functional potential of the human microbiome. Studies have linked microbiome composition to various health conditions, including obesity, diabetes, inflammatory bowel disease, and mental health disorders. Understanding these associations opens avenues for personalized medicine and microbiome-based therapies. A study by [60] used metagenomics to compare the gut microbiomes of obese and lean individuals. The research identified specific microbial signatures associated with obesity, providing insights into potential therapeutic targets for metabolic disorders. Through metagenomic techniques, microbial profiles in patients with inflammatory bowel disease (IBD) were compared to those of healthy individuals. The study suggested that alterations in the gut microbiome could contribute to the pathogenesis of IBD [61](Table 2).

Table 2 . Metagenomics research that has impacted the economy of Africa through Health.

Study AreaCountryKey FindingsOutcomeReferences
Pathogens
Detection		Poland
Singapore
Tanzania
Uganda
South Africa		Human herpesvirus 1 (HHV-1) was detected unexpectedly while searching for RNA viruses. NGS can identify both RNA and DNA pathogens from CSFNGS, alongside nucleic acid amplification, can enhance the diagnostic approach for encephalitis.
Pathogen detection and disease surveillance		[63]
[66]
[71]
[72]
[73]
Human microbiome and Health predictionDenmark
USA
Kenya
Tunisia, South Africa, Morocco, Egypt, Ghana, China, Spain, Germany
Cameroon		Higher bacterial rDNA in obese individuals' liver samples. A strong correlation between bacterial rDNA load and fatty liver index
Discovery of novel genes with potential biotechnological and therapeutic applications, including antimicrobial compounds.
Strong positive correlation of S. infantis with blood glucose levels		Increased bacterial DNA in obese livers may be an early risk factor for the progression of non-alcoholic fatty liver disease (NAFLD)
Consistent changes in microbiome structure and function across regions; implications for microbiome-based therapies for IBD Bioengineered Probiotics and novel therapeutics in human medicine
Demonstrated specific intra-individual modifications in gut microbiome associated with metabolic and inflammatory improvements post-surgery.
gut microbiota as a therapeutic target for GDM		[60]
[74]
[59]
[17]
[75]
[61]
[25]
[19]
[13]
[71]
Human antibioticresistant bacteriaMultiple (collaborative research involving institutions from Jordan, Malaysia, USA, Nigeria, Kuwait, Saudi Arabia, UAE, and Pakistan)
South Africa Canada		High prevalence of antibiotic resistance in various bacterial strains
Importance of rapid and accurate detection methods to combat AMR		Recommendations for improved detection strategies and the need for ongoing research in AMR diagnostics.
Identification of new antibiotic producers		[69]
[65]
[70]
[68]


Contribution of metagenomics to disease surveillance and pathogen discovery

In Africa, genomics has shown to be a priceless tool for pathogen detection and disease surveillance, assisting in the resolution of some of the most urgent health issues facing the region. The capacity of metagenomic techniques to rapidly and comprehensively identify a wide range of pathogens, including those difficult to culture or identify using traditional diagnostic methods, is one of their primary advantages. The unbiased metagenomic approach to identifying emerging pathogens and tracking outbreaks is remarkable. Metagenomic sequencing of clinical samples can also provide insights into antimicrobial resistance genes, guiding treatment strategies and public health interventions. For instance, metagenomic sequencing was utilized in a study that identified Crimean-Congo Hemorrhagic Fever Virus (CCHFV) that was causing an acute hemorrhagic fever outbreak in Uganda [62]. Through the analysis of patient blood samples, the virus was quickly identified and a diagnostic test was developed, enabling more efficient public health responses. In a study by [63], metagenomics was used to identify a novel virus responsible for the mysterious outbreak of encephalitis. The rapid identification of the pathogen facilitated appropriate public health responses and containment measures (Table 2).

Another study on antimicrobial resistance by [64] employed metagenomics to monitor the spread of antibiotic-resistant genes in hospital wastewater. The findings underscored the importance of environmental surveillance in combating antimicrobial resistance. Antimicrobial resistance (AMR) in microbial communities has also been tracked using metagenomic techniques, which have given important new information about the distribution and prevalence of AMR genes [65]. The initiatives to stop the spread of AMR can be informed by this knowledge, which makes it crucial for stewardship efforts. For instance, a metagenomic analysis of Nigerian sewage samples revealed that the frequency of AMR genes was considerably greater in urban than in rural areas, underscoring the necessity of focused interventions to address this escalating public health concern [53].

Apart from its application in disease surveillance and outbreak research, metagenomics has yielded several hitherto unidentified viruses, bacteria, and other microbes that may have consequences for the health of humans, animals, and the environment [66]. For example, several new species of cyanobacteria were found through a metagenomic analysis of the microbial communities of Lake Victoria, Africa's biggest freshwater lake that may have consequences for human health and water quality [42]. Additionally, metagenomics can be used to investigate how microbial communities are affected by pollution, climate change, and other environmental issues, as well as possible health implications for humans. For instance, exposure to oil pollution was linked to changes in the composition and function of microbial communities, which may have consequences for human health, according to a metagenomic study of the microbial communities in the Niger Delta, one of the most polluted areas of Africa [67].

The rise of antibiotic-resistant bacteria poses a significant threat to global health. Metagenomics allows for the comprehensive assessment of antibiotic-resistance genes in various environments, including hospitals, wastewater, and agricultural settings. This information is essential for understanding the spread of resistance and developing strategies to mitigate its impact. A study by [18] utilized metagenomics to profile antibiotic resistance genes in hospital settings. The research identified reservoirs of resistance genes, informing infection control practices and antibiotic stewardship programs. Metagenomics analysis by [48] also revealed the prevalence of antibiotic-resistance genes in agricultural soils treated with manure. The findings highlighted the role of agricultural practices in the dissemination of resistance genes and the need for sustainable management strategies (Table 2). In general, metagenomics has great promise for enhancing health outcomes in Africa, ranging from identifying and tracking infections and antibiotic resistance to finding new microorganisms and evaluating environmental health.

Impact on public health policies and preventive measures

Early warning systems and illness surveillance could be greatly enhanced by the use of metagenomics in the African health sector. Metagenomic data can provide a deeper understanding of the microbial ecosystem, aiding in the development of robust disease surveillance networks to detect established and emerging diseases more effectively. By improving surveillance capacity, quicker detection and response to disease outbreaks can reduce their impact and enhance public health outcomes. Targeted public health treatments can also be developed using insights from metagenomics. Metagenomic research, for instance, can assist in identifying particular microbe targets for vaccine production, guiding the creation of more successful immunization plans [68].

Similarly, metagenomic analysis of patterns of antimicrobial resistance can guide the development of specialized antimicrobial stewardship initiatives, encouraging the prudent use of medicines and preventing the spread of illnesses resistant to drugs [69]. Furthermore, the development of focused initiatives to increase access to clean water and sanitation and hence lessen the burden of waterborne diseases can be guided by metagenomic data on pathogens associated with water and sanitation [70].

In addition to enhancing disease surveillance and intervention methods, metagenomic studies foster collaborative research and knowledge sharing by utilizing the information and resources available worldwide, genome research conducted in Africa has the potential to further improve public health outcomes through international collaborations and knowledge exchange.

The transformative potential of metagenomics for Africa's Economic future

The comprehensive study of genetic material collected directly from environmental samples, or metagenomics, has great potential to propel sustainable economic development throughout Africa. Metagenomics is a cutting-edge scientific field that offers African countries a special chance to open up new avenues for innovation, diversification, and international competitiveness. Through the application of metagenomic research ideas, African nations have the potential to transform their agricultural methods, increasing crop yields and decreasing dependency on imported commodities. The discovery of helpful microorganisms that can improve plant resistance and soil fertility may result in the creation of environmentally friendly biopesticides and fertilizers, better food security, increased farm incomes, and improved population health and nutrition are all possible outcomes of this, and they are all essential for promoting long-term economic stability throughout the continent [76].

To address urgent health issues like antibiotic resistance and infectious diseases, researchers can create more focused and efficient therapies by developing a greater understanding of the complex microbial ecosystems within the human body. Beyond the fields of medicine and agriculture, metagenomics has the potential to promote innovation and economic diversification in Africa. The production of value-added goods, biofuels, and other biotechnological applications can result from the discovery of novel microbial resources and biomolecules, creating new export markets and supporting the expansion of developing businesses. African countries can enhance their standing in the global knowledge economy by attracting foreign investments, talent, and knowledge transfers by positioning themselves as leaders in metagenomics research and development [77]. However, realizing the full economic potential of metagenomics in Africa will require strategic investments, collaborative partnerships, and the establishment of robust supporting infrastructure. Governments, research institutions, and private sector organizations must work together to address the persistent challenges, such as limited research capabilities, insufficient funding, and the need for capacity building in bioinformatics and genomic research.

In addition, Africa's position as a major global economic partner can be reinforced through the sharing of metagenomics data and insights to aid international efforts in addressing critical issues such as food security, disease control, and environmental conservation. Through the adoption of this cutting-edge field, African countries can open up new opportunities for innovation, diversification, and sustainable growth, which will ultimately improve the resilience and prosperity of their communities in the context of the global economy.

Challenges and future prospects in implementing metagenomic studies

Despite its promise, metagenomics faces several challenges. These include the complexity of data analysis, the need for standardized protocols, and the interpretation of functional potential from sequence data. Future research should focus on integrating metagenomic data with other omics approaches, such as metatranscriptomics, and metabolomics, to gain a holistic understanding of microbial communities [74]. It is obvious from this review that, there is limited literature on metagenome application in biofuel and the gut microbiome of agriculture farm animals. Additionally, advancements in single-cell genomics and synthetic biology could further enhance the applications of metagenomics in agriculture and health.

While metagenomics has great promise for transforming sustainable development in Africa, effective implementation of metagenomic investigations is hampered by several technical and infrastructure issues. Many African nations lack access to high-throughput sequencing equipment and bioinformatics expertise, posing one of the biggest obstacles [78]. Inadequate funding for research and investment in building the lab infrastructure, tools, and training programs required to enable metagenomics research represents another significant obstacle. Overcoming these obstacles can also be greatly aided by partnerships and collaborations between scholars, institutions, and organizations in Africa and beyond. African researchers can obtain access to the newest sequencing technologies, bioinformatics tools, training, and mentorship possibilities by utilizing the knowledge and assets of foreign partners [79].

Another setback is inconsistent power supplies and internet connectivity in some areas that might cause delays and problems in the workflow and data processing associated with metagenomic investigations. Standardized procedures and quality control methods for sample handling, collecting, and analysis should also be developed to guarantee data comparability and reliability. Highly qualified workers such as computational biologists and bioinformaticians are required to evaluate the intricate metagenomic datasets and turn the results into useful insights.

Metagenomics can potentially revolutionize sustainable development in Africa through its application in public health, renewable energy, and agriculture. Researchers can gain insights into the ecological and functional aspects of microbial communities by sequencing and analyzing their genetic material. [2]. This can lead to creative solutions for urgent problems in a variety of industries. Metagenomics has the potential to uncover bacteria in agriculture that enhance soil fertility, boost crop productivity, and minimize the application of chemical pesticides and fertilizers [33]. Within the field of renewable energy, metagenomic research has the potential to expedite the identification of novel enzymes and microorganisms that optimize biomass conversion and biofuel production efficiency. Metagenomics also has the potential to support public health initiatives such as tailored medicine delivery, innovative pharmaceutical development, and infectious disease identification and surveillance.

Strategic investments in research and development, capacity building, infrastructure enhancements, and cooperative relationships between African academics, institutions, and international stakeholders can all help to overcome these challenges. African nations may develop local metagenomics competence and expertise by bridging the gap in resources and skills. This will lead to innovations that benefit local people and promote a more just and sustainable global economy. To ensure the responsible and equitable use of metagenomics, ethical considerations must be properly addressed in addition to technological and infrastructure challenges [80]. The full potential of metagenomics can be fully realized while protecting the rights and interests of local communities through the implementation of robust data governance policies, transparent criteria for obtaining consent, and fair benefit-sharing mechanisms. Continued research and interdisciplinary collaboration are essential to fully realize the potential of metagenomics in addressing global challenges.

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