Early-life chemical exposome and gut microbiome development: African research perspectives within a global environmental health context

African neonates, infants, and toddlers (NITs) may be exposed to a multitude of environmental chemicals that may impact their gut microbiota (GM) and health into adulthood.Acute and chronic long-term effects of fermented foods, delivery environment, and herbal mixtures on the GM of NITs need to be systematically investigated.Understanding the interactions between dietary and environmental exposures and the developing GM should be a research focus on the continent. The gut microbiome of neonates, infants, and toddlers (NITs) is very dynamic, and only begins to stabilize towards the third year of life. Within this period, exposure to xenobiotics may perturb the gut environment, thereby driving or contributing to microbial dysbiosis, which may negatively impact health into adulthood. Despite exposure of NITs globally, but especially in Africa, to copious amounts and types of xenobiotics – such as mycotoxins, pesticide residues, and heavy metals – little is known about their influence on the early-life microbiome or their effects on acute or long-term health. Within the African context, the influence of fermented foods, herbal mixtures, and the delivery environment on the early-life microbiome are often neglected, despite being potentially important factors that influence the microbiome. Consequently, data on in-depth understanding of the microbiome–exposome interactions is lacking in African cohorts. Collecting and evaluating such data is important because exposome-induced gut dysbiosis could potentially favor disease progression. The gut microbiome of neonates, infants, and toddlers (NITs) is very dynamic, and only begins to stabilize towards the third year of life. Within this period, exposure to xenobiotics may perturb the gut environment, thereby driving or contributing to microbial dysbiosis, which may negatively impact health into adulthood. Despite exposure of NITs globally, but especially in Africa, to copious amounts and types of xenobiotics – such as mycotoxins, pesticide residues, and heavy metals – little is known about their influence on the early-life microbiome or their effects on acute or long-term health. Within the African context, the influence of fermented foods, herbal mixtures, and the delivery environment on the early-life microbiome are often neglected, despite being potentially important factors that influence the microbiome. Consequently, data on in-depth understanding of the microbiome–exposome interactions is lacking in African cohorts. Collecting and evaluating such data is important because exposome-induced gut dysbiosis could potentially favor disease progression. The human gut is a complex and dynamic ecosystem that contains trillions of microorganisms [1.Qin J. et al.A human gut microbial gene catalogue established by metagenomic sequencing.Nature. 2010; 464: 59-65Crossref PubMed Scopus (6957) Google Scholar]. Typically, bacteria are numerically dominant [2.Stewart C.J. et al.Temporal development of the gut microbiome in early childhood from the TEDDY study.Nature. 2018; 562: 583-588Crossref PubMed Scopus (666) Google Scholar] but, certain fungal genera [3.Pérez J.C. Fungi of the human gut microbiota: roles and significance.Int. J. Med. Microbiol. 2021; 3111514990Crossref PubMed Scopus (11) Google Scholar] and viruses and phages [4.Camarillo-Guerrero L.F. et al.Massive expansion of human gut bacteriophage diversity.Cell. 2021; 184: 1098-1109.e9Abstract Full Text Full Text PDF PubMed Scopus (98) Google Scholar] are also present. Recent advances in next generation sequencing technologies have led to an upsurge of research interest in exploring the human gut microbiota (HGM) (see Glossary). As such, scientists are only beginning to understand the depth and complexity of the HGM and its importance in human health. Mounting evidence points to the involvement of the HGM in a multitude of pathophysiological conditions, including asthma [5.Depner M. et al.Maturation of the gut microbiome during the first year of life contributes to the protective farm effect on childhood asthma.Nat. Med. 2020; 26: 1766-1775Crossref PubMed Scopus (87) Google Scholar], colorectal cancer [6.Jahani-Sherafat S. et al.Role of gut microbiota in the pathogenesis of colorectal cancer; a review article.Gastroenterol. Hepatol. 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In African cohorts, the HGM has been implicated in playing a role in severe malnutrition in children [9.Nabwera H.M. et al.Interactions between fecal gut microbiome, enteric pathogens, and energy regulating hormones among acutely malnourished rural Gambian children.EBioMedicine. 2021; 73103644Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar] as well as the severity of neglected tropical diseases such as schistosomiasis [10.Ajibola O. et al.Urogenital schistosomiasis is associated with signatures of microbiome dysbiosis in Nigerian adolescents.Sci. Rep. 2019; 9: 829Crossref PubMed Scopus (19) Google Scholar,11.Osakunor D.N.M. et al.The gut microbiome but not the resistome is associated with urogenital schistosomiasis in preschool-aged children.Commun. Biol. 2020; 3: 155Crossref PubMed Scopus (7) Google Scholar]. Environmental exposures, such as to dietary chemicals, can have profound effect on the composition of the HGM [12.Wilson A.S. et al.Diet and the human gut microbiome: an international review.Dig. Dis. Sci. 2020; 65: 723-740Crossref PubMed Scopus (100) Google Scholar]. Generally, the diet of neonates, infants, and toddlers (NITs) includes breast milk nutrition within the first 6 months [13.WHO Global Strategy for Infant and Young Child Feeding.Fifty-fourth World Health Assembly. World Health Organization, 2003Google Scholar], followed by complementary foods and then solid foods. In some parts of Africa, large amounts of xenobiotics can contaminate complementary foods [14.Ojuri O.T. et al.Assessing the mycotoxicological risk from consumption of complementary foods by infants and young children in Nigeria.Food Chem. 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In addition, foods can contain bioactive compounds such as polyphenols [18.Oesterle I. et al.Polyphenol exposure, metabolism, and analysis: a global exposomics perspective.Annu. Rev. Food Sci. Technol. 2021; 12: 461-484Crossref PubMed Scopus (6) Google Scholar]. Given that the gut is a major contact point between food and microorganisms [19.Livovsky D.M. et al.Food, eating, and the gastrointestinal tract.Nutrients. 2020; 12: 986Crossref Scopus (13) Google Scholar], the HGM of NITs is exposed to both beneficial nutrients and chemicals with toxic or bioactive properties. The composition of the HGM in the first 3 years of life is highly dynamic [2.Stewart C.J. et al.Temporal development of the gut microbiome in early childhood from the TEDDY study.Nature. 2018; 562: 583-588Crossref PubMed Scopus (666) Google Scholar]. Moreover, within this age group, exposure to high concentrations of xenobiotics can lead to dysbiosis-induced issues with immune system maturation [20.Olin A. et al.Stereotypic immune system development in newborn children.Cell. 2018; 174: 1277-1292Abstract Full Text Full Text PDF PubMed Scopus (286) Google Scholar]. Research in animal models suggests that xenobiotics can induce compositional and functional changes in the HGM [21.Wang J.J. et al.Metagenomic analysis of gut microbiota alteration in a mouse model exposed to mycotoxin deoxynivalenol.Toxicol. Appl. Pharmacol. 2019; 372: 47-56Crossref PubMed Scopus (17) Google Scholar, 22.Yan W. et al.Individual and combined toxicogenetic effects of microplastics and heavy metals (Cd, Pb, and Zn) perturb gut microbiota homeostasis and gonadal development in marine medaka (Oryzias melastigma).J. Hazard. 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Consequently, exposome-induced gut dysbiosis in NITs may be involved in adverse health outcomes later in life [27.Arrieta M.C. et al.Early infancy microbial and metabolic alterations affect risk of childhood asthma.Sci. Transl. Med. 2015; 7307ra152Crossref PubMed Scopus (894) Google Scholar], especially in high-risk regions such as rural African communities. Although xenobiotic contaminants in food constitutes a serious health risk, it is largely unknown how xenobiotics influence the HGM development in NITs, especially in resource-scarce rural communities in sub-Saharan Africa, where exposure to toxic chemicals is often high [28.Ezekiel C.N. et al.Dietary risk assessment and consumer awareness of mycotoxins among household consumers of cereals, nuts and legumes in north-central Nigeria.Toxins. 2021; 13: 635Crossref PubMed Scopus (5) Google Scholar, 29.Sager M. et al.Heavy metal content and element analysis of infant formula and milk powder samples purchased on the Tanzanian market: international branded versus black market products.Food Chem. 2018; 255: 365-371Crossref PubMed Scopus (17) Google Scholar, 30.Mekonen S. et al.Exposure of infants to organochlorine pesticides from breast milk consumption in southwestern Ethiopia.Sci. Rep. 2021; 1122053Crossref Scopus (1) Google Scholar]. Apart from a Tanzanian study that investigated the influence of probiotic yogurt on toxic metals vis-à-vis changes in gut microbiome in school children (6–10 years of age) [31.Bisanz J.E. et al.Randomized open-label pilot study of the influence of probiotics and the gut microbiome on toxic metal levels in Tanzanian pregnant women and school children.mBio. 2014; 5e01580-14Crossref PubMed Scopus (114) Google Scholar], little is known about chemical exposome–early-life microbiome interactions on the continent. As HGM research continues to evolve globally, studies on interactions between xenobiotics and the early-life HGM in African cohorts should be a research priority. To the best of our knowledge, there is no comprehensive review of microbiome studies of African NITs nor review of the impact of xenobiotics on the early-life HGM in African cohorts. This review is therefore intended to: (i) provide an overview of HGM diversity in African NITs, (ii) discuss factors influencing the microbiota, with specific consideration of the Africa context, (iii) identify research gaps, (iv) identify reasons for the limited amount of research into early-life HGM exposomics on the continent, and (iv) provide possible solutions to the highlighted problems. The HGM is generally similar among individuals, especially at the phylum taxonomic rank, but differences can occur with respect to the dominant phylum. Moreover, differences occur in HGM at lower taxonomic rank (genus, species, and strain levels). With respect to abundant taxa, the most common bacteria detected in the stool of African NITs include plant-polysaccharide-degrading Prevotella, human-milk oligosaccharide-metabolizing Bifidobacterium, to taxa containing commensals as well as pathogens such as Escherichia/Shigella (Table 1). However, HGM composition can be affected by factors such as diet type, frequency and level of exposure to xenobiotics, delivery mode, hygiene practices and NIT health (Table 1). Later, a subset of these exposures and factors are briefly discussed and new research insights within the African setting are provided. Certain xenobiotics are highlighted in this review due to the availability of data and frequent detection in biofluids from NITs (Table 2), whereas emphasis on fermented foods, herbal mixtures, and delivery environment is based on their potential 'crucial-yet-overlooked' roles in influencing NITs' gut microbiota.Table 1Overview of bacterial diversity in African neonates, infants and toddlers' stool within the past decade (2011–2021)Region/countryAgeOverview of genera/species diversityPublished dominant/higher abundance genus/speciesPossible contributory factor to bacterial diversityStudy focusMethod of identificationRefsNorth AfricaEgypt2.5–12 yearsBacteroides, Bifidobacterium, Clostridium difficile, Desulfovibrio, Lactobacillus, Prevotella, Ruminococcus, SutterellaBacteroidesaHigher abundance in children diagnosed with autism spectrum disorder.RuminococcusaHigher abundance in children diagnosed with autism spectrum disorder.NAAutism spectrum disorderReal-time PCR[87.Ahmed S.A. et al.Study of the gut microbiome profile in children with autism spectrum disorder: a single tertiary hospital experience.J. Mol. Neurosci. 2020; 70: 887-896Crossref PubMed Scopus (17) Google Scholar]West AfricaNigeria<3yearsBacteroides, Bifidobacterium, Blautia,Catenibacterium, Collinsella Coprococcus, Clostridium, Dialister, Faecalibacterium, Haemophilus, Klebsiella Lachnobacterium, Lachnospira Lactobacillus, Prevotella, Phascolarctobacterium, Ruminococcus, SuccinivibrioSutterella, VeillonellaBifidobacteriumbHigher abundance in urban population.VeillonellabHigher abundance in urban population.PrevotellacHigher abundance in rural population.Diet, lifestyle, hygiene practicesComparison between rural and urban population16S rRNA sequencing[34.Ayeni F.A. et al.Infant and adult gut microbiome and metabolome in rural Bassa and urban settlers from Nigeria.Cell Rep. 2018; 23: 3056-3067Abstract Full Text Full Text PDF PubMed Scopus (77) Google Scholar]Nigeria2 weeksAcinetobacter baumannii, Aeromonas hydrophilia, Bacteroides fragilis, Clostridium, Citrobacter koseri, coagulase-negative Staphylococcus, Enterobacter aerogenes, Enterobacter cloacae, Enterobacter intermedius, Escherichia coli, Klebsiella oxytoca, Staphylococcus aureus, Proteus mirabilis, Raoultella ornitholytica, Serratia fanticola, Serratia liquefaciensStaphylococcus aureus, Escherichia coliMode of deliveryBacterial diversity in the first 2 weeks of lifeAPI[88.Kigbu A. et al.Intestinal bacterial colonization in the first 2 weeks of life of Nigerian neonates using standard culture methods.Front. Pediatr. 2016; 4: 139Crossref PubMed Scopus (7) Google Scholar]Ghana6 weeksAllistipes, Bacteroides, Coprococcus, Eubacterium, Prevotella, Ruminococcus, Streptococcus bovis, Tannerella,BacteroidesdCorrelated with lack of rota virus vaccine response., PrevotelladCorrelated with lack of rota virus vaccine response., Streptococcus boviseCorrelated with rota virus vaccine response.NACorrelation between gut microbiome and response to rotavirus vaccineHITChip microarray[89.Harris V.C. et al.Significant correlation between the infant gut microbiome and rotavirus vaccine response in rural Ghana.J. Infect. Dis. 2017; 215: 34-41Crossref PubMed Scopus (172) Google Scholar]Burkina Faso6–59 monthsAnaerococcus, Bacteroides, Blautia, Butyricimonas, Camplylobacter, Catenibacterium, Clostridium, Coprococcus, Dialister, Finegoldia, Klebsiella, Lachnospira, Megasphaera, Oscillospira, Peptoniphilus, Phascolarctobacterium, Porphyromonas, Prevotella, Roseburia, Ruminococcus, Streptococcus, SuccinivibrioPrevotellafDominant at both baseline and post-treatment.Use of antibioticsEffects of antibiotics on microbial diversity16S rRNA sequencing[48.Oldenburg C.E. et al.Effect of commonly used pediatric antibiotics on gut microbial diversity in preschool children in Burkina Faso: a randomized clinical trial.Open Forum Infect Dis. 2018; 5ofy289Crossref Scopus (22) Google Scholar]Gabon<1 monthAcinetobacter, Amphibacillus, Bacteroides, Bradyrhizobium, Collinsella, Enterococcus, Herbaspirillum, Jeotgalicoccus, Klebsiella Ornithinicoccus, Prevotella, Sarcina, Segetibacter, StreptococcusPrevotellagDominant in the first day of life.Mode of delivery, dietBacterial/viral diversity during the first month of life16S rRNA sequencing[35.Brazier L. et al.Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life.PLoS One. 2017; 12e0185569Crossref PubMed Scopus (11) Google Scholar]Gambia6–24 monthsEnterobacteriaceae, Escherichia-Shigella, Haemophilus, LactobacillusEnterobacteriaceaehEnriched in children suffering from non-edematous severe acute malnutrition.NAInteractions between fecal microbiome and acute malnutrition16S rRNA sequencing, qPCR[9.Nabwera H.M. et al.Interactions between fecal gut microbiome, enteric pathogens, and energy regulating hormones among acutely malnourished rural Gambian children.EBioMedicine. 2021; 73103644Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar]Guinea-Bissau2–15Campylobacter, Clostridium clades, Collinsella, Lactobacillus, Prevotella, Ruminococcus, VeillonellaCampylobacteriIncreased abundance with protozoan infection., PrevotellajAssociated with Giardia lamblia infection, Clostridium IVkIncreased abundance with infection with Entamoeba histolytica/dispar and Entamoeba nana.NAIntestinal protozoan infections and bacterial microbiota16S rRNA sequencing[90.von Huth S. et al.Intestinal protozoan infections shape fecal bacterial microbiota in children from Guinea-Bissau.PLoS Negl. Trop. Dis. 2021; 15e0009232Crossref PubMed Scopus (5) Google Scholar]Senegal0–5 yearsBacillus, Bacteroides, Clostridium, Enterococcus, Escherichia coliClostridiumlMore frequent among children without diarrhea.BacillusmMore frequent among children with diarrhea.NAMicrobial diversity of people with and without diarrheaMALDI-TOF, 16S rRNA sequencing[91B. Samb-Ba, et al., MALDI-TOF identification of the human gut microbiome in people with and without diarrhea in Senegal, PLoS One, 9, e87419.Google Scholar]Cote d'Ivoire10–75 daysAkkermansia, Bacteroides fragilis, Bacteroides thetaiotaomicron, Bifidobacterium longum, B. bifidum, B. breve, Clostridium paraputrificum, Collinsella aerofaciens, E. coli, Klebsiella quasipneumoniae, Klebsiella pneumoniae, Prevotella, Phocaeicola coprophilus, Streptococcus, Veillonella párvula, V. seminalisBifidobacterium longum, B. bifidum, E. coli.Diet, Geographical locationMicrobial diversity of infants living in suburban areas16S rRNA sequencing, Shot gun metagenomics[92.Fontana F. et al.Investigating the infant gut microbiota in developing countries: worldwide metagenomic meta-analysis involving infants living in sub-urban areas of Côte d'Ivoire.Environ. Microbiol. Rep. 2021; 13: 626-636Crossref PubMed Scopus (0) Google Scholar]Niger1–60 monthsAnaerovibrio, Bifidobacterium, Blautia, Clostridium, Collinsella, Escherichia, Faecalibacterium, Megasphaera, Peptoniphilus, Prevotella, Roseburia, Ruminococcus, SuccinivibrioFaecalibacteriumnAbundant at both baseline and after antibiotic treatment., BlautianAbundant at both baseline and after antibiotic treatment.BifidobacteriumoThird most abundant genera.Use of antibioticsInfluence of azithromycin on gut microbiome diversity16S rRNA sequencing[49.Doan T. et al.Gut microbial diversity in antibiotic-naive children after systemic antibiotic exposure: a randomized controlled trial.Clin. Infect. Dis. 2017; 64: 1147-1153Crossref PubMed Scopus (41) Google Scholar]Niger1–59 monthsAnaerococcus, Bacteroides, Brachyspira, Bifidobacterium, Campylobacter, Clostridium, Escherichia, Faecalibacterium, Helicobacter, Megasphaera, Porphyromonas, PrevotellaStudy focused on CampylobacterUse of antibioticsInfluence of antibiotics on gut microbiome compositionMetagenomic RNA sequencing[93.Doan T. et al.Gut microbiome alteration in MORDOR I: a community-randomized trial of mass azithromycin distribution.Nat. Med. 2019; 25: 1370-1376Crossref PubMed Scopus (48) Google Scholar]Central AfricaCentral African Republic2–5 yearsAggregatibacter, Allisonella, Campylobacter, Fusobacterium, Morococcus, Prevotella, Streptococcus, Shigella/E. coli, VeillonellaCampylobacterpPrevalent in stunted children., Escherichia coli/ShigellapPrevalent in stunted children.Age, country of originChildhood stunting16S rRNA sequencing[94.Vonaesch P. et al.Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa.Proc. Natl. Acad. Sci. U. S. A. 2018; 115: E8489-E8498Crossref PubMed Scopus (83) Google Scholar]Republic of Congo1 monthAcinetobacter, Amphibacillus, Bacteroides, Bradyrhizobium, Collinsella, Enterococcus, Herbaspirillum, Jeotgalicoccus, Klebsiella Ornithinicoccus, Prevotella, Sarcina, Segetibacter, StreptococcusPrevotellaqDominant within the first days of life.Mode of delivery, dietBacterial/viral diversity during the first month of life16S rRNA sequencing[35.Brazier L. et al.Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life.PLoS One. 2017; 12e0185569Crossref PubMed Scopus (11) Google Scholar]East AfricaEthiopiaBifidobacterium, Clostridium sensu stricto 1, Escherichia/Shigella, Klebsiella, Lactobacillus, Streptococcus, VeillonellaLactobacillusrHigh relative abundance in rural settings.DietComparison between human milk and infant fecal microbiota16S rRNA sequencing[95.Lackey K.A. et al.What's normal? microbiomes in human milk and infant feces are related to each other but vary geographically: the inspire study.Front. Nutr. 2019; 6: 45Crossref PubMed Scopus (84) Google Scholar]Kenya5.5 monthsBacteroides, Bifidobacteriaceae, Clostridium difficile, C. perfringens, Escherichia/Shigella, Enterobacteriaceae, Faecalibacterium, Lactobacillus, Prevotella, Salmonella, StreptococcusBifidobacteriaceaesDominant at 6 months.Escherichia/ShigellatHigh abundance in infants receiving micronutrient powder at endpoint.DietInfluence of iron fortification on gut microbiome of anemic and non-anemic infants16S rRNA pyrosequencing, qPCR[96.Jaeggi T. et al.Iron fortification adversely affects the gut microbiome, increases pathogen abundance and induces intestinal inflammation in Kenyan infants.Gut. 2015; 64: 731-742Crossref PubMed Scopus (365) Google Scholar]Tanzania<1 monthBifidobacterium, EnterobacteriaceaeBifidobacteriumDietInfluence of probiotic yogurt on fecal microbiota16S rRNA sequencing[97.Bisanz J.E. et al.Microbiota at multiple body sites during pregnancy in a rural Tanzanian population and effects of moringa-supplemented probiotic yogurt.Appl. 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Microbiol. 2015; 81: 4965-4975Crossref PubMed Scopus (54) Google Scholar]Uganda17 months (mean age)Acinetobacter, Bacteroides, Blautia, Campylobacter, Clostridium, Comamonas, Coprococcus, Dialister, Enterobacter, Enterobacteriaceae, Faecalibacterium prausnitzii, Haemophilus, Haemophilus parainfluenzae, Klebsiella, Lachnospira, Lactobacillus ruminis, Moraxellaceae, Oscillospira, Prevotella, Ruminococcus, VeillonellaEnterobacteriaceaeuHigher distribution in children suffering from diarrhea.MoraxellaceaeuHigher distribution in children suffering from diarrhea.FaecalibacteriumvAbundant in children admitted with severe acute malnutrition after treatment and discharge., BlautiavAbundant in children admitted with severe acute malnutrition after treatment and discharge.Diarrhea, probiotic treatmentInfluence of probiotics on gut microbiota of severe acute malnourished children16S rRNA sequencing[41.Castro-Mejía J.L. et al.Restitution of gut microbiota in Ugandan children administered with probiotics (Lactobacillus rhamnosus GG and Bifidobacterium animalis subsp. lactis BB-12) during treatment for severe acute malnutrition.Gut Microbes. 2020; 11: 855-867Crossref PubMed Scopus (20) Google Scholar]Southern AfricaMalawi6 monthsBifidobacterium longum, B. bifidum, B. breve, Bacteroides-Prevotella, Clostridium histolyticumBifidobacteriumDiet, geographical locationGut microbiota diversity in rural populationqPCR, flow cytometry-FISH[98.Grzeskowiak L. et al.Distinct gut microbiota in southeastern African and northern European infants.J. Pediatr. Gastroenterol. Nutr. 2012; 54: 812-816Crossref PubMed Scopus (121) Google Scholar]Malawi6–12 monthsBacteroides, Bifidobacterium, Collinsella, Dialister, Escherichia/Shigella, Lactobacillus mucosae, L. ruminis, Megasphaera, Megasphaera elsdenii, Olsenella, Prevotella, Prevotella copri, Streptococcus, VeillonellaBifidobacteriumwAbundant at 7.5 months.PrevotellaxAbundant at 10.5 months.AgeInfluence of legume supplementation on gut microbiota16S rRNA sequencing[99.Ordiz M.I. et al.The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months.Am. J. Clin. Nutr. 2020; 111: 884-892Crossref PubMed Scopus (4) Google Scholar]Malawi6, 12, 18 monthsActinomyces, Atopobium, Campylobacter, Clostridium, Enterobacter, Eubacterium, Faecalibacterium, Klebsiella, Lactococcus, Lactobacillus, Leuconostoc, Ruminococcus, Salmonella, Slackia, Streptococcus, PrevotellaBacteroidesyAssociated with WAZ between 6 and 12 months. ClostridiumyAssociated with WAZ between 6 and 12 months. EubacteriumyAssociated with WAZ between 6 and 12 months. PrevotellayAssociated with WAZ between 6 and 12 months. RuminococcusyAssociated with WAZ between 6 and 12 months.NAAssociation of gut microbiota with growth and inflammation16S rRNA sequencing[100.Kamng'ona, A.W. et al.The association of gut microbiota characteristics in Malawian infants with growth and inflammation.Sci. Rep. 2019; 912893PubMed Google Scholar]Zambia6–24 monthsBacteroides, Bifidobacteria, Enterococcus, LactobacillusBacteroideszHigher abundant in children who consume fermented beverages., LactobacilluszHigher abundant in children who consume fermented beverages.DietInfluence of traditional fermented foods on gut microbial compositionqPCR(J. Chileshe, PhD thesis, Wageningen University, 2019)Zimbabwe18 monthsBacteroides thetaiotaomicron, Bacteroides ovatus, Bifidobacterium bifidum, B. pseudocatenulanum, B. longum, Collinsella aerofaciens, Escherichia coli, Streptococcus mitis, Streptococcus pneumoniae, Staphylococcus hominis,B. longumNAGut microbiome and oral rotavirus vaccine immunogenicityMetagenome Shotgun sequencing[101.Robertson R.C. et al.The fecal microbiome and rotavirus vaccine immunogenicity in rural Zimbabwean infants.Vaccine. 2021; 39: 5391-5400Crossref PubMed Scopus (3) Google Scholar]Mozambique≤14 days–12 monthsBacteroides, Bifidobacterium, Clostridium coccoides, C. leptum, Enterococcus, Lactobacillus, Streptococcus, Staphylococcus aureus, S. epidermidisBifidobacterium, Streptococci, EnterococciDiet, ageMicrobial diversity of infants in a high HIV prevalent areaqPCR[102.González R. et al.Breast milk and gut microbiota in African mothers and infants from an area of high HIV prevalence.PLoS One. 2013; 8e80299Crossref Scopus (58) Google Scholar]South Africa18 months (mean age)Cronobacter, Enterococcus Escherichia, Klebsiella, Listeria, StreptococcusEscherichia coli, E. faeciumaaDominant in the gastrointestinal disease group., Klebsiella pneumoniaeabAbundant in respiratory disease group.DiseaseFecal microbiota of infants with respiratory, gastrointestinal and other diseases16S rRNA sequencing[103.Krishnamoorthy S. et al.Dysbiosis signatures of fecal microbiota in South African infants with respiratory, gastrointestinal, and other diseases.J. Pediatr. 2020; 218: 106-113Abstract Full Text Full Text PDF PubMed Scopus (7) Google Scholar]Abbreviations: API, analytical profile index; HITChip microarray, highly reproducible phylogenetic fingerprinting microarray; MALDI-TOF, matrix-assisted laser desorption/ionization-time of flight; NA, not available; qPCR, quantitative polymerase chain reaction.a Higher abundance in children diagnosed with autism spectrum disorder.b Higher abundance in urban population.c Higher abundance in rural population.d Correlated with lack of rota virus vaccine response.e Correlated with rota virus vaccine response.f Dominant at both baseline and post-treatment.g Dominant in the first day of life.h Enriched in children suffering from non-edematous severe acute malnutrition.i Increased abundance with protozoan infection.j Associated with Giardia lamblia infectionk Increased abundance with infection with Entamoeba histolytica/dispar and Entamoeba nana.l More frequent among children without diarrhea.m More frequent among children with diarrhea.n Abundant at both baseline and after antibiotic treatment.o Third most abundant genera.p Prev