Organic waste substrates induce important shifts in gut microbiota of black soldier fly (Hermetia illucens L.) : coexistence of conserved, variable, and potential pathogenic microbes

The sustainable utilization of black soldier fly (BSF) for recycling organic waste into nutrient-rich biomass such as high-quality protein additive, is gaining momentum. Its gut microbiota is thought to play an important role. The study provides the first comprehensive analysis of bacterial and fungal communities of BSF gut across untreated substrates and highlights conserved members, potential pathogens, and their interactions. Findings show most bacteria found in the BSF gut are transient, and are affected by the local environment. The study contributes to establishment of safety measures for future processing of BSF larval meals and the creation of legislation to regulate their use in animal feeds.Australian Centre for International Agricultural Research (ACIAR)Norwegian Agency for Development CooperationNetherlands Organization for Scientific ResearchWOTRO Science for Global Development (NWO-WOTRO)The Rockefeller Foundatio

Loss and gain of gut bacterial phylotype symbionts in afrotropical stingless bee species (Apidae: Meliponinae)

Stingless bees (Apidae: Meliponini) are the most diverse group of corbiculate bees and are important managed and wild pollinators distributed in the tropical and subtropical regions of the globe. However, little is known about their associated beneficial microbes that play major roles in host nutrition, detoxification, growth, activation of immune responses, and protection against pathogens in their sister groups, honeybees and bumble bees. Here, we provide an initial characterization of the gut bacterial microbiota of eight stingless bee species from sub-Saharan Africa using 16S rRNA amplicon sequencing. Our findings revealed that Firmicutes, Actinobacteria, and Proteobacteria were the dominant and conserved phyla across the eight stingless bee species. Additionally, we found significant geographical and host intra-species-specific bacterial diversity. Notably, African strains showed significant phylogenetic clustering when compared with strains from other continents, and each stingless bee species has its own microbial composition with its own dominant bacterial genus. Our results suggest host selective mechanisms maintain distinct gut communities among sympatric species and thus constitute an important resource for future studies on bee health management and host-microbe co-evolution and adaptation.Figure S1: Alpha rarefaction curve. Figure S2: Gut bacterial genera associated with each of the eight stingless bee species in Kenya. Figure S3: Bacterial alpha diversity did not correlate with the stingless bee size. Table S1: 16S rRNA sequencing data analysis (Excel file).Supplementary material: Figure S1: Alpha rarefaction curve. Figure S2: Gut bacterial genera associated with each of the eight stingless bee species in Kenya. Figure S3: Bacterial alpha diversity did not correlate with the stingless bee size. Table S1: 16S rRNA sequencing data analysis (Excel file).The Swiss National Science Foundation Postdoc Mobility, the German Academic Exchange Service (DAAD), Norwegian Agency for Development Cooperation, the Section for Research, Innovation, and Higher Education and by icipe core donors.https://www.mdpi.com/journal/microorganismsam2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Organic waste substrates induce important shifts in gut microbiota of black soldier fly (Hermetia illucens L.) : coexistence of conserved, variable, and potential pathogenic microbes

The sustainable utilization of black soldier fly (BSF) for recycling organic waste into nutrient-rich biomass, such as high-quality protein additive, is gaining momentum, and its microbiota is thought to play important roles in these processes. Several studies have characterized the BSF gut microbiota in different substrates and locations; nonetheless, in-depth knowledge on community stability, consistency of member associations, pathogenic associations, and microbe–microbe and host–microbe interactions remains largely elusive. In this study, we characterized the bacterial and fungal communities of BSF larval gut across four untreated substrates (brewers’ spent grain, kitchen food waste, poultry manure, and rabbit manure) using 16S and ITS2 amplicon sequencing. Results demonstrated that substrate impacted larval weight gain from 30 to 100% gain differences among diets and induced an important microbial shift in the gut of BSF larvae: fungal communities were highly substrate dependent with Pichia being the only prevalent genus across 96% of the samples; bacterial communities also varied across diets; nonetheless, we observed six conserved bacterial members in 99.9% of our samples, namely, Dysgonomonas, Morganella, Enterococcus, Pseudomonas, Actinomyces, and Providencia. Among these, Enterococcus was highly correlated with other genera including Morganella and Providencia. Additionally, we showed that diets such as rabbit manure induced a dysbiosis with higher loads of the pathogenic bacteria Campylobacter. Together, this study provides the first comprehensive analysis of bacterial and fungal communities of BSF gut across untreated substrates and highlights conserved members, potential pathogens, and their interactions. This information will contribute to the establishment of safety measures for future processing of BSF larval meals and the creation of legislation to regulate their use in animal feeds.The Canadian International Development Research Centre (IDRC) and the Australian Centre for International Agricultural Research (ACIAR), Norwegian Agency for Development Cooperation, the Section for Research, Innovation, and Higher Education (CAP-Africa), the Netherlands Organization for Scientific Research, WOTRO Science for Global Development (NWO-WOTRO) and The Rockefeller Foundation through the International Centre of Insect Physiology and Ecology (icipe).http://www.frontiersin.org/Microbiologyam2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Characterization of the honey bee and stingless bee gut microbiota: A hidden diversity and host-specific microbiomes from sub-Saharan-African region

Pollinators are significant contributors to world’s economy, nutrition, food security and biodiversity. Among all animal pollinators, the honey bee, Apis mellifera, is one of the most important and widely used managed pollinators worldwide, while stingless bees (Apidae: Meliponini) are becoming important alternative pollinators of horticulture crops, particularly with the recent honey bee colony losses worldwide. Recently, attention has been drawn to the microbiota communities associated with bee gut and their potential impact on the host physiology and health. However, no comprehensive study on this subject has been conducted in Africa, where important native diversity of the bees is found. Here, I characterized the gut microbiota of honey bee and stingless bee species/sub-species from sub-Saharan Africa using 16S rRNA amplicon sequence. In honey bees, I found all the core gut microbiota members reported elsewhere in the world, bees from the coastal regions of Kenya harbours a higher relative abundance and diversity of core members than bees from other regions. Additionally, I showed that Gilliamella, Snodgrassella and Frischella dominated in all locations, and that altitude and humidity affect Gilliamella abundance. In contrast, I found that Lactobacillus was less common compared to temperate regions of the world. In stingless bees, I found that Firmicutes, Actinobacteria and Proteobacteria were the dominant and conserved phyla across the eight studied species. Nevertheless, I found significant continent-specific and host intra-species diversity where each stingless bee species has a distinct gut composition, and African bacterial strains cluster together based on phylogeny. Furthermore, I established protocols in the laboratory for newly emerged microbe-deprived worker bee rearing, and bee mono-inoculation. Using these protocols, I showed that Commensalibacter sp. AMU001 effectively colonized and multiplied in the bee gut and it did not affect its survival. This study is a first comprehensive study of the gut microbiota of bees from sub-Saharan Africa. The data and protocols develop in this thesis represent an important step towards the development of state-of-the-art bee gut microbiota research in Africa. Additionally, results will guide future strategies to improve bee health in the continent, the development of potential probiotics to increase bee resistance against pest and pathogens, to improve bee nutrition, and increase resilience against climate change.Thesis (PhD (Molecular Biology and Biotechnology))--University of Pretoria, 2020.The Newton-Utafiti grant from the British Council (reference 275898413) and German Academic Exchange Service (DAAD) In-Region Postgraduate Scholarship (reference 91671945); icipe core funding provided by UK Aid from the UK Government, Swedish International Development Cooperation Agency (Sida), Swiss Agency for Development and Cooperation (SDC), Federal Democratic Republic of Ethiopia, and the Government of Kenya.GeneticsPhD (Molecular Biology and Biotechnology)Unrestricte

Loss and Gain of Gut Bacterial Phylotype Symbionts in Afrotropical Stingless Bee Species (Apidae: Meliponinae)

Stingless bees (Apidae: Meliponini) are the most diverse group of corbiculate bees and are important managed and wild pollinators distributed in the tropical and subtropical regions of the globe. However, little is known about their associated beneficial microbes that play major roles in host nutrition, detoxification, growth, activation of immune responses, and protection against pathogens in their sister groups, honeybees and bumble bees. Here, we provide an initial characterization of the gut bacterial microbiota of eight stingless bee species from sub-Saharan Africa using 16S rRNA amplicon sequencing. Our findings revealed that Firmicutes, Actinobacteria, and Proteobacteria were the dominant and conserved phyla across the eight stingless bee species. Additionally, we found significant geographical and host intra-species-specific bacterial diversity. Notably, African strains showed significant phylogenetic clustering when compared with strains from other continents, and each stingless bee species has its own microbial composition with its own dominant bacterial genus. Our results suggest host selective mechanisms maintain distinct gut communities among sympatric species and thus constitute an important resource for future studies on bee health management and host-microbe co-evolution and adaptation

Characterization of the Kenyan Honey Bee (Apis mellifera) Gut Microbiota: A First Look at Tropical and Sub-Saharan African Bee Associated Microbiomes

Gut microbiota plays important roles in many physiological processes of the host including digestion, protection, detoxification, and development of immune responses. The honey bee (Apis mellifera) has emerged as model for gut-microbiota host interaction studies due to its gut microbiota being highly conserved and having a simple composition. A key gap in this model is understanding how the microbiome differs regionally, including sampling from the tropics and in particular from Africa. The African region is important from the perspective of the native diversity of the bees, and differences in landscape and bee management. Here, we characterized the honey bee gut microbiota in sub-Saharan Africa using 16S rRNA amplicon sequencing. We confirm the presence of the core gut microbiota members and highlight different compositions of these communities across regions. We found that bees from the coastal regions harbor a higher relative abundance and diversity on core members. Additionally, we showed that Gilliamella, Snodgrassella, and Frischella dominate in all locations, and that altitude and humidity affect Gilliamella abundance. In contrast, we found that Lactobacillus was less common compared temperate regions of the world. This study is a first comprehensive characterization of the gut microbiota of honey bees from sub-Saharan Africa and underscores the need to study microbiome diversity in other indigenous bee species and regions.</jats:p