Comparison of bacterial diversity in wheat bran and in the gut of larvae and newly emerged adult of Musca domestica (Diptera: Muscidae) by use of ethidium monoazide reveals bacterial colonization

Effect of Ciprofloxacin on the Composition of Intestinal Microbiota in Sarcophaga peregrina (Diptera: Sarcophagidae)

The intestinal bacteria of insects are crucial to the growth and development of the host. It has been found that various physiological processes of insects, such as immune response, metabolism, reproductive ability, and growth and development, involve the gastrointestinal flora. However, many external factors affect the composition of insects' intestinal microorganisms, such as the type of dietary substrate. Sarcophaga peregrina (Robineau-Desvoidy, 1830) (Diptera: Sarcophagidae) is of great significance in medicine and forensic science. In this study, we investigated the effects of ciprofloxacin on the growth and gut microbiota of S. peregrina. The results demonstrated that the maximum body length of larvae was not affected by ciprofloxacin, while the growth rate of body length quickened as the concentration of the drug increased. The weight of the pupa and adult was reduced significantly due to the effect of ciprofloxacin. After analyzing the gut microbiota composition of S. peregrina in different drug groups, it was indicated that Ignatzschineria, Providencia, Wohlfahrtiimonas, Proteus, Myroides, and Bacteroides play important roles in the growth of S. peregrina. However, they still need to be further studied. In general, ciprofloxacin can affect the gut microbial community structure, which in turn affects the fitness of the host.

Pathogenicity of multiple Providencia species (Enterobacteriales: Morganellaceae) to the mass-reared Mexican fruit fly (Diptera: Tephritidae)

Mexican fruit fly (Anastrepha ludens (Loew)) (Diptera: Tephritidae) represents a major threat to fruit production in the Western Hemisphere. Sterile insect technique is used to suppress and eradicate wild populations. Success of this control method necessitates weekly production of hundreds of millions of flies, their sterilization by irradiation, and their aerial release. Diet needed to produce large fly numbers are conducive to the spread of bacteria. Pathogenic bacteria were isolated from 3 rearing facilities and from multiple sources: eggs, larvae, pupae and spent diet, and were found to include some isolates identified to the genus Providencia (Enterobacteriales: Morganellaceae). We identified 41 Providencia isolates and tested their pathogenicity to A. ludens. Based on 16s rRNA sequences, 3 groups were clustered into several species of Providencia with varying capacities to affect the Mexican fruit fly production. Isolates putatively identified as P. alcalifaciens/P. rustigianii were all pathogenic causing larval and pupal yield reduction of 46-64% and 37-57%, respectively. Among them, Providencia isolate 3006 was the most pathogenic reducing larval and pupae yield by 73 and 81%, respectively. Isolates identified as P. sneebia were not pathogenic. The final cluster, P. rettgeri/P. vermicola, were variable in pathogenicity with 3 isolates yielding like the control and the rest causing larval and pupal yield reduction of 26-53% and 23-51%, respectively. Isolates putatively identified as P. alcalifaciens/P. rustigianii were more virulent than P. rettgeri/P. vermicola. Accurate identification of species is needed to diagnose and monitor pathogenic versus nonpathogenic Providencia strains.

A full-scale black soldier fly larvae (Hermetia illucens) bioconversion system for domestic biodegradable wastes to resource

Domestic biodegradable wastes (DBW) pose a threat to environmental quality and human health. Bioconversion via black soldier fly larvae (BSFL; Hermitia illucens L.) is an expedient way for converting 'waste to resource' (insect protein and biofertilizer). Although researches abounded in laboratory-reared experiments and bioconversion mechanisms were pertinent, the void of data from actual and full-scale operation restricts the intensification of BSFL technology and its global adoption. Hence, a full-scale BSFL bioconversion system lasting 4 years in Hangzhou (China) was investigated, and the feasibility and efficiency of 15 tonnes of DBW per day were studied. Through continuous technical optimization, the average production of fresh larvae was increased from 8.5% in 2017 to 15.3% in 2020, along with bioconversion rate of final vermicompost decreased from 35.4% to 14.5%. The total biomass reduction rate in 2020 was 68.7 ± 17.4 kg/(m³ d), equivalent to 0.735 ± 0.215 kg/(kg d) in the form of fresh larvae. Crude fat in fresh larvae accounted for 13.4%, and crude protein accounted for 16.2% in which the determined amino acid profile bore a strong resemblance to fish meal only except histidine and tyrosine. Its economic benefits proved the feasibility of this technology, and the profit reached up to 35.9 US$ per tonne of DBW in 2019. In conclusion, BSFL bioconversion system under current 'insect-farm' operation was a promising solution for DBW treatment with value-added waste recycling.

Effects of habitat and sampling time on bacterial community composition and diversity in the gut of the female house fly, Musca domestica Linnaeus (Diptera: Muscidae)

Adult house flies feed and breed in a variety of microbe-rich habitats and serve as vectors for human and animal pathogens. To better understand their role in harbouring and disseminating bacteria, we characterized the composition and diversity of bacterial communities in the gut of female house flies collected from three different habitats in Kansas: agricultural (dairy farm), urban (business area dumpsters) and mixed (business located between residential and animal agriculture areas). Bacterial community composition and diversity were influenced more by the house flies' habitat than by sampling time. The most abundant taxa were also highly prevalent in the house flies collected from all three habitats, potentially representing a 'core microbiome' attributable to the fly's trophic and reproductive associations with substrates and food sources comprised of decaying matter and/or animal waste. Bacterial taxa associated with vertebrate guts/faeces and potential pathogens were highly abundant in agricultural fly microbial communities. Interestingly, taxa of potential pathogens were highly abundant in flies from the mixed and urban sites. House flies harboured diverse bacterial communities influenced by the habitat in which they reside, including potential human and animal pathogens, further bolstering their role in the dissemination of pathogens, and indicating their utility for pathogen surveillance.

Effects of feeding on different parts of Ailanthus altissima on the intestinal microbiota of Eucryptorrhynchus scrobiculatus and Eucryptorrhynchus brandti (Coleoptera: Curculionidae)

Eucryptorrhynchus brandti and Eucryptorrhynchus scrobiculatus (Coleoptera: Curculionidae) are two monophagous weevil pests that feed on Ailanthus altissima (Mill.) Swingle but differ in their diet niche. In the field, adults of E. brandti prefer to feed on the trunk of A. altissima, whereas adults of E. scrobiculatus prefer to feed on the tender parts. We conducted Illumina sequencing of 16S rRNA to examine changes in bacterial diversity in the adults of these two weevil species after they fed on different parts of A. altissima (trunk, 2–3-year-old branches, annual branches, and petioles). Proteobacteria, Tenericutes, and Firmicutes were the dominant phyla in E. brandti (relative abundance was 50.64, 41.56, and 5.63%, respectively) and E. scrobiculatus (relative abundance was 78.63, 11.91, and 7.41%, respectively). At the genus level, Spiroplasma, endosymbionts2, Unclassified Enterobacteriaceae, and Lactococcus were dominant in E. brandti, and Unclassified Enterobacteriaceae, Wolbachia and Spiroplasma, and endosymbionts2 were dominant in E. scrobiculatus. Linear discriminant analysis effect size analysis revealed microbial biomarkers in the different treatment group of adults of both weevil species. Adults of E. brandti may require the trunk, and adults of E. scrobiculatus may require the petioles and annual branches to maintain the high diversity of their gut microbes. The results of this study indicate that feeding on different parts of A. altissima affects the composition and function of the microbes of E. brandti and the microbial composition of E. scrobiculatus. Variation in the abundance of Wolbachia and Spiroplasma in E. brandti and E. scrobiculatus is associated with dietary niche changes, and this might explain the evolution of reproductive isolation between these two sibling weevil species.

Houseflies harbor less diverse microbiota under laboratory conditions but maintain a consistent set of host-associated bacteria

The housefly (Musca domestica) is a wide-ranging insect, often associated with decaying matter from livestock and humans. The septic environments in which houseflies live are believed to be a rich source for microbial acquisition. Although the housefly can harbor a wide range of microorganisms, it is not yet well known which microbes are always recurrent, which are dispensable and which environmentally dependent. In the present study, we aim at identifying which microbes are recurrently associated with the housefly gut throughout the species’ life cycle and whether their acquisition relies on the fly’s living environment. We surveyed three housefly strains—two of them kept under standard laboratory conditions for a long time and one wild-caught. To track any shifts happening throughout the lifecycle of the housefly and to test the consistency of the revealed microbial communities, we sampled houseflies at five developmental stages over the course of four consecutive generations. Both the bacterial and fungal microbiota of five developmental stages were studied for all samples, using amplicon sequencing for the 16S and ITS1 rRNA gene, respectively. Results revealed diverse microbial communities yet consistent for each of the two distinct sampling environments. The wild-caught population showed a more diverse and more distinct gut microbiota than the two laboratory strains, even though the strain was phylogenetically similar and shared geographic origin with one of them. Two bacterial genera, Myroides and Providencia, and two yeasts, Trichosporon and Candida tropicalis, were present in all sampled larvae and pupae, regardless of the strain. Analysis of the provided diet revealed that the flies acquired the yeasts through feeding. Our main findings show that houseflies might lose microbial diversity when reared in controlled environments, however they can maintain a consistent set of bacteria. We conclude that although the environment can facilitate certain microbial transmission routes for the housefly, and despite the fungal microbiota being largely acquired through diet, the larval bacterial gut microbiome remains relatively consistent within the same developmental stage.

Enterobacter hormaechei in the intestines of housefly larvae promotes host growth by inhibiting harmful intestinal bacteria

BACKGROUND

As a pervasive insect that transmits a variety of pathogens to humans and animals, the housefly has abundant and diverse microbial communities in its intestines. These gut microbes play an important role in the biology of insects and form a symbiotic relationship with the host insect. Alterations in the structure of the gut microbial community would affect larval development. Therefore, it is important to understand the mechanism regulating the influence of specific bacteria on the development of housefly larvae.

METHODS

For this study we selected the intestinal symbiotic bacterium Enterobacter hormaechei, which is beneficial to the growth and development of housefly larvae, and used it as a probiotic supplement in larval feed. 16S rRNA gene sequencing technology was used to explore the effect of E. hormaechei on the intestinal flora of housefly larvae, and plate confrontation experiments were performed to study the interaction between E. hormaechei and intestinal microorganisms.

RESULTS

The composition of the gut microflora of the larvae changed after the larvae were fed E. hormaechei, with the abundance of Pseudochrobactrum, Enterobacter and Vagococcus increasing and that of Klebsiella and Bacillus decreasing. Analysis of the structure and interaction of larval intestinal flora revealed that E. hormaechei inhibited the growth of harmful bacteria, such as Pseudomonas aeruginosa, Providencia stuartii and Providencia vermicola, and promoted the reproduction of beneficial bacteria.

CONCLUSIONS

Our study has explored the influence of specific beneficial bacteria on the intestinal flora of houseflies. The results of this study reveal the important role played by specific beneficial bacteria on the development of housefly larvae and provide insight for the development of sustained biological agents for housefly control through interference of gut microbiota.

Endosymbiotic Bacteria Aid to Overcome Temperature Induced Stress in the Oriental Fruit Fly, Bactrocera dorsalis

Endosymbiotic microbiota are known to have an enormous impact on their host, influencing its physiology, behavior, fitness, and various other aspects. The present study hypothesizes that certain bacterial symbionts aid the Oriental fruit fly, Bactrocera dorsalis in its adaptation to survive thermal stress encountered in the environment. Investigative studies on the change in gut and reproductive tract microbiota diversity of male and female B. dorsalis revealed that certain genera of Acinetobacter, Brevibacillus, Bacillus, Enterobacter, Enterococcus, Pseudomonas, and Staphylococcus were involved in the adaptation of B. dorsalis to temperature stresses. The intestinal and reproductive tract bacterial community of B. dorsalis varied depending on the temperature the insects were reared at. We hypothesized that the microbiota present in B. dorsalis' gut helped it endure temperature stresses over prolonged periods. Out of 54 bacterial isolates, 25, 15, and 14 isolates were obtained from flies reared at 27 °C, 18 °C, and 35 °C, respectively. A 16S rDNA analysis revealed that the bacterial isolates (reared at different temperatures) belonged to different genera. The flies were supplemented with antibiotics to suppress the existing gut microbiota and subsequently fed with bacterial isolates from flies reared at 18 °C, 27 °C (control) or 35 °C separately. When these flies were placed in incubators pre-set at the above temperatures, the survival rate exhibited by the flies differed significantly. The flies fed with bacterial isolates from 18 °C could survive only in incubators pre-set at 18 °C, while flies fed with bacterial isolates from 35 °C could survive only at 35 °C and not vice versa. The microbiota supplementation assay established that the presence of specific bacterial isolates aided the flies' survival under varied thermal stresses.

A Molecular Survey of Bacterial Species in the Guts of Black Soldier Fly Larvae (Hermetia illucens) Reared on Two Urban Organic Waste Streams in Kenya

Globally, the expansion of livestock and fisheries production is severely constrained due to the increasing costs and ecological footprint of feed constituents. The utilization of black soldier fly (BSF) as an alternative protein ingredient to fishmeal and soybean in animal feed has been widely documented. The black soldier fly larvae (BSFL) used are known to voraciously feed and grow in contaminated organic wastes. Thus, several concerns about their safety for inclusion into animal feed remain largely unaddressed. This study evaluated both culture-dependent sequence-based and 16S rDNA amplification analysis to isolate and identify bacterial species associated with BSFL fed on chicken manure (CM) and kitchen waste (KW). The bacteria species from the CM and KW were also isolated and investigated. Results from the culture-dependent isolation strategies revealed that Providencia sp. was the most dominant bacterial species detected from the guts of BSFL reared on CM and KW. Morganella sp. and Brevibacterium sp. were detected in CM, while Staphylococcus sp. and Bordetella sp. were specific to KW. However, metagenomic studies showed that Providencia and Bordetella were the dominant genera observed in BSFL gut and processed waste substrates. Pseudomonas and Comamonas were recorded in the raw waste substrates. The diversity of bacterial genera recorded from the fresh rearing substrates was significantly higher compared to the diversity observed in the gut of the BSFL and BSF frass (leftovers of the rearing substrates). These findings demonstrate that the presence and abundance of microbiota in BSFL and their associated waste vary considerably. However, the presence of clinically pathogenic strains of bacteria in the gut of BSFL fed both substrates highlight the biosafety risk of potential vertical transmission that might occur, if appropriate pre-and-postharvest measures are not enforced.

Negative Impact of Pseudomonas aeruginosa Y12 on Its Host Musca domestica

High concentrations of Pseudomonas aeruginosa Y12 significantly inhibit the development of housefly larvae and accelerate larvae death. In this study, the dynamic distribution of the gut microbiota of housefly larvae fed different concentrations of P. aeruginosa Y12 was investigated. Compared with low-concentration P. aeruginosa diets, orally administered high-concentration P. aeruginosa diets caused higher mortality and had a greater impact on the community structure and interaction network of intestinal flora in housefly larvae. The bacterial community of the gut microbiota in housefly larvae was reconstructed in 4 days. Bacterial abundance and diversity were significantly reduced in housefly larvae fed high concentrations of P. aeruginosa. With the growth of larvae, the relative abundances of Providencia, Proteus, Myroides, Klebsiella, and Alcaligenes increased significantly in housefly larvae fed with high concentrations of P. aeruginosa, while the relative abundances of Bordetella, Enterobacter, Morganella, Ochrobactrum, Alcaligenaceae, and Empedobacter were significantly reduced. To analyze the role of the gut microorganisms played on housefly development, a total of 10 cultivable bacterial species belonging to 9 genera were isolated from the intestine of housefly larvae among which Enterobacter hormaechei, Klebsiella pneumoniae, Enterobacter cloacae, Lysinibacillus fusiformis, and Bacillus safensis promoted the growth of larvae through feeding experiments. This study is the first to analyze the influence of high concentrations of P. aeruginosa on the gut microbiota of houseflies. Our study provides a basis for exploring the pathogenic mechanism of high concentrations of P. aeruginosa Y12 in houseflies.

Characteristics and nutrient function of intestinal bacterial communities in black soldier fly (Hermetia illucens L.) larvae in livestock manure conversion

The potential utility of black soldier fly larvae (BSFL) to convert animal waste into harvested protein or lipid sources for feeding animal or producing biodiesel provides a new strategy for agricultural waste management. In this study, the taxonomic structure and potential metabolic and nutrient functions of the intestinal bacterial communities of BSFL were investigated in chicken and swine manure conversion systems. Proteobacteria, Firmicutes and Bacteroidetes were the dominant phyla in the BSFL gut in both the swine and chicken manure systems. After the larvae were fed manure, the proportion of Proteobacteria in their gut significantly decreased, while that of Bacteroidetes remarkably increased. Compared with the original intestinal bacterial community, approximately 90 and 109 new genera were observed in the BSFL gut during chicken and swine manure conversion, and at least half of the initial intestinal genera found remained in the gut during manure conversion. This result may be due to the presence of specialized crypts or paunches that promote microbial persistence and bacteria-host interactions. Ten core genera were found in all 21 samples, and the top three phyla among all of the communities in terms of relative abundance were Proteobacteria, Firmicutes and Bacteroidetes. The nutrient elements (OM, TN, TP, TK and CF) of manure may partly affect the succession of gut bacterial communities with one another, while TN and CF are strongly positively correlated with the relative abundance of Providencia. Some bacterial taxa with the reported ability to synthesize amino acids, Rhizobiales, Burkholderia, Bacteroidales, etc., were also observed in the BSFL gut. Functional analysis based on genes showed that intestinal microbes potentially contribute to the nutrition of BSFL and the high-level amino acid metabolism may partly explain the biological mechanisms of protein accumulation in the BSFL body. These results are helpful in understanding the biological mechanisms of high-efficiency nutrient conversion in BSFL associated with intestinal microbes.

Identification of Bacteria in Two Food Waste Black Soldier Fly Larvae Rearing Residues

Significant economic, environmental, and social impacts are associated with the avoidable disposal of foods worldwide. Mass-rearing of black soldier fly (Hermetia illucens) larvae using organic wastes and food- and agro-industry side products is promising for recycling resources within the food system. One current challenge of this approach is ensuring a reliable and high conversion performance of larvae with inherently variable substrates. Research has been devoted to increasing rearing performance by optimizing substrate nutrient contents and ratios, while the potential of the substrate and larval gut microbiota to increase rearing performance remains untapped. Since previous research has focused on gut microbiota, here, we describe bacterial dynamics in the residue (i.e., the mixture of frass and substrate) of black soldier fly larvae reared on two food wastes (i.e., canteen and household waste). To identify members of the substrate and residue microbiota, potentially associated with rearing performance, bacterial dynamics were also studied in the canteen waste without larvae, and after inactivation by irradiation of the initial microbiota in canteen waste. The food waste substrates had similar microbiota; both were dominated by common lactic acid bacteria. Inactivation of the canteen waste microbiota, which was dominated by Leuconostoc, Bacillus, and Staphylococcus, decreased the levels of all rearing performance indicators by 31-46% relative to canteen waste with the native microbiota. In both food waste substrates, larval rearing decreased the bacterial richness and changed the physicochemical residue properties and composition over the rearing period of 12 days, and typical members of the larval intestinal microbiota (i.e., Providencia, Dysgonomonas, Morganella, and Proteus) became more abundant, suggesting their transfer into the residue through excretions. Future studies should isolate members of these taxa and elucidate their true potential to influence black soldier fly mass-rearing performance.

Comparison of microbiota, antimicrobial resistance genes and mobile genetic elements in flies and the feces of sympatric animals

Flies are well-known vectors of bacterial pathogens, but there are little data on their role in spreading microbial community and antimicrobial resistance. In this study, we compared the bacterial community, antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in flies with those in the feces of sympatric animals. A 16S rRNA-based microbial analysis identified 23 bacterial phyla in fecal samples and 25 phyla in flies; all the phyla identified in the fecal samples were also found in the flies. Bray-Curtis dissimilarity analysis showed that the microbiota of the flies were more similar to the microbiota of the feces of their sympatric animals than those of the feces from the three other animal species studied. The qPCR array amplified 276 ARGs/MGEs in fecal samples, and 216 ARGs/MGEs in the flies, while 198 of these genes were identified in both flies and feces. Long-term studies with larger sample numbers from more geospatially distinct populations and infection trials are indicated to further evaluate the possibility of flies as sentinels for antimicrobial resistance.

Comparative analysis of gut bacterial communities in housefly larvae fed different diets using a high-throughput sequencing approach

Housefly larvae are a synanthropic host for various bacteria, including pathogens and commensals and an important protein source for monogastric animal feed. Many factors, such as diets, life stages, host habitats can influence microbial community structure. In this study, the diversity of bacterial communities in the gut of housefly larvae fed on different artificial diets was comprehensively characterized using high-throughput sequencing with the aim shedding light on an optimal larval diet. The results showed that the dominant bacteria belonging to Proteobacteria, Firmicutes and Bacteroidetes phyla were related to polysaccharide degradation. The comparative analysis indicated that the dominant intestinal bacteria of larvae fed on high-protein were similar to those on high-fat diet. The same was the case in larvae fed high-starch diet and wheat bran alone. In addition, the diversity of intestinal bacteria at genus level in larvae fed high-protein and high-fat diet was higher than in larvae fed the other two diets. Further analysis indicated that the increase of potential commensals and decrease of pathogens in larvae fed on high-fat diet contributed to the increase of housefly larvae immunity. It established a foundation for further research on improvement of nutrition of housefly larvae used for poultry and fish feed.

Housefly (Musca domestica L.) associated microbiota across different life stages

The housefly (Musca domestica L.) lives in close association with its microbiota and its symbionts are suggested to have pivotal roles in processes such as metabolism and immune response, but it is unclear how the profound physiological changes during ontogeny affect the housefly’s associated microbiota and their metabolic capabilities. The present study applies 16S rRNA gene amplicon sequencing to investigate the development of the host-associated microbiota during ontogeny. The potential for microbiota transfer between developmental stages, and the metabolic potential of these microbiota were evaluated. Representatives of Firmicutes were observed as early colonisers during the larval stages, followed by colonisation by organisms affiliating with Proteobacteria and Bacteroidetes as the flies matured into adults. Microbiota observed across all the developmental stages included Lactococcus, Lactobacillus and Enterococcus, while Weissella and Chishuiella were associated with newly hatched larvae and adults, respectively. Predictive metabolic profiling of the identified microorganisms further suggested that the microbiota and their functional profile mature alongside their host and putative host-microbe relationships are established at different stages of development. The predicted metabolic capability of the microbiota developed from primarily simple processes including carbohydrate and nucleotide metabolisms, to more complex metabolic pathways including amino acid metabolisms and processes related to signal transduction.

Decomposition of biowaste macronutrients, microbes, and chemicals in black soldier fly larval treatment: A review

Processing of biowaste with larvae of the black soldier fly, Hermetia illucens L. (Diptera: Stratiomyidae), is an emerging waste treatment technology. Larvae grown on biowaste can be a relevant raw material for animal feed production and can therefore provide revenues for financially viable waste management systems. In addition, when produced on biowaste, insect-based feeds can be more sustainable than conventional feeds. Among others, the scalability of the technology will depend on the availability of large amounts of biowaste with a high process performance (e.g. bioconversion of organic matter to proteins and lipids) and microbial and chemical product safety. Currently, in contrast to other waste treatment technologies, such as composting or anaerobic digestion, the process performance is variable and the processes driving the decomposition of biowaste macronutrients, inactivation of microbes and fate of chemicals is poorly understood. This review presents the first summary of the most important processes involved in black soldier fly larvae (BSFL) treatment, based on the available knowledge concerning five well-studied fly species. This is a starting point to increase understanding regarding the processes of this technology, with the potential to increase its efficiency and uptake, and support the development of appropriate regulations. Based on this review, formulating different types of biowaste, e.g. to produce a diet with a similar protein content, a balanced amino acid profile and/or pre- and co-treatment of biowaste with beneficial microbes, has the potential to increase process performance. Following harvest, larvae require heat or other treatments for microbial inactivation and safety.

The gut bacteria across life stages in the synanthropic fly Chrysomya megacephala

BACKGROUND

Gut bacteria are closely associated with host. Chrysomya megacephala, as a vector and resource insect, can transmit various pathogenic bacteria and consume manure to produce biofertilizer and larva biomass. However, the gut bacteria composition and abundance of C. megacephala remain unclear.

RESULTS

Illumina MiSeq platform was used to compare composition of gut bacterial community in eggs, 1-day-old larvae, 5-day-old larvae, pupae, adult females and males by sequencing with variation in V4 region of 16S ribosomal DNA gene. In total, 928 operational taxonomic units (OTUs) were obtained. These OTUs were annotated into 19 phyla, 42 classes, 77 orders, 153 families and 289 genera. More than 0.5% abundance of 32 OTU core genera were found across all life stages. At class level, Alphaproteobacteria, Bacilli, Bacteroidia, Betaproteobacteria, Flavobacteriia and Gammaproteobacteria were the most abundant in C. megacephala. Eight species were identified to have significantly different abundance between 1-d-larvae and 5-day-larvae and took 28.95% of shared species between these two groups. Sex-specific bacterial species were identified that Faecalibacterium prausnitzii was merely present in females, while Rhodococcus fascians was merely present in males.

CONCLUSION

Gut bacteria of C. megacephala varied across life stages. The composition and community structure of the bacterial community differed from young larvae to mature larvae, while that were similar in adult females and males. These data will provide an overall view of bacterial community across life stages in C. megacephala with attention on manure associated and pathogenic bacteria.

Ignatzschineria cameli sp. nov., isolated from necrotic foot tissue of dromedaries (Camelus dromedarius) and associated maggots (Wohlfahrtia species) in Dubai

Five bacterial strains, UAE-HKU57^T, UAE-HKU58, UAE-HKU59, UAE-HKU60 and UAE-HKU61, were isolated in Dubai, UAE, from necrotic foot tissue samples of four dromedaries (Camelus dromedarius) and associated maggots (Wohrlfartia species). They were non-sporulating, Gram-negative, non-motile bacilli. They grew well under aerobic conditions at 37 °C, but not anaerobically. The pH range for growth was pH 7.0-9.0 (optimum, pH 7.5-8.0) and the strains could tolerate NaCl concentrations (w/v) up to 2 % (optimum, 0.5 %). They were catalase- and cytochrome oxidase-positive, but caseinase-, gelatinase- and urease-negative. Their phenotypic characters were distinguishable from other closely related species. Phylogenetic analyses of the almost-complete 16S rRNA gene and partial 23S rRNA gene, gyrB, groEL and recA sequences revealed that the five isolates were most closely related to undescribed Ignatzschineria strain F8392 and Ignatzschineria indica, but in most phylogenies clustered separately from these close relatives. Average nucleotide identity analysis showed that genomes of the five isolates (2.47-2.52 Mb, G+C content 41.71-41.86 mol%) were 98.00-99.97% similar to each other, but ≤87.18 % similar to other Ignatzschineriaspecies/strains. Low DNA relatedness between the five isolates to other Ignatzschineriaspecies/strains was also supported by Genome-to-Genome Distance Calculator analysis. The chemotaxonomic traits of the five strains were highly similar. They were non-susceptible (intermediate or resistant) to tetracycline and resistant to trimethoprim/sulphamethoxazole. The name Ignatzschineria cameli sp. nov. is proposed to accommodate these five strains, with strain UAE-HKU57^T (=CCOS1165^T=NBRC 113042^T) as the type strain.

The gut microbiota in larvae of the housefly Musca domestica and their horizontal transfer through feeding

House fly larvae provide a prolific and sustainable source of proteins used in poultry and fish feed. Wheat bran is a superior diet for house fly larvae and has been widely investigated to exploit its potential in the food and feed area. Using Illumina MiSeq 16S rDNA sequencing, this study investigated the gut microbiota of house fly larvae feeding on wheat bran and the bacterial community in the wheat bran. The bacterial communities in the house fly larvae were dominated by the phyla Proteobacteria and Firmicutes. Enterobacteriaceae and Providencia were the predominant bacteria at the family and genus levels, respectively. Some bacteria in the phyla Actinobacteria, Proteobacteria, Bacteroidetes and Firmicutes may be transferred from the gut of house flies to the wheat bran during feeding and may be involved in degrading and utilizing polysaccharides in the cell wall of wheat bran. The significance of the gut microbiota of house fly larvae, their transferring and roles in degradation of wheat bran is discussed. These findings regarding the gut microbiota of house fly larvae will provide opportunities for research on the impact of microbial communities on poultry and fish.

Bacterial Communities Associated with Houseflies (Musca domestica L.) Sampled within and between Farms

The housefly feeds and reproduces in animal manure and decaying organic substances and thus lives in intimate association with various microorganisms including human pathogens. In order to understand the variation and association between bacteria and the housefly, we used 16S rRNA gene amplicon sequencing to describe bacterial communities of 90 individual houseflies collected within and between ten dairy farms in Denmark. Analysis of gene sequences showed that the most abundant classes of bacteria found across all sites included Bacilli, Clostridia, Actinobacteria, Flavobacteria, and all classes of Proteobacteria and at the genus level the most abundant genera included Corynebacterium, Lactobacillus, Staphylococcus, Vagococcus, Weissella, Lactococcus, and Aerococcus. Comparison of the microbiota of houseflies revealed a highly diverse microbiota compared to other insect species and with most variation in species richness and diversity found between individuals, but not locations. Our study is the first in-depth amplicon sequencing study of the housefly microbiota, and collectively shows that the microbiota of single houseflies is highly diverse and differs between individuals likely to reflect the lifestyle of the housefly. We suggest that these results should be taken into account when addressing the transmission of pathogens by the housefly and assessing the vector competence variation under natural conditions.

The antibiotic resistome of swine manure is significantly altered by association with the Musca domestica larvae gut microbiome

The overuse of antibiotics as veterinary feed additives is potentially contributing to a significant reservoir of antibiotic resistance in agricultural farmlands via the application of antibiotic-contaminated manure. Vermicomposting of swine manure using housefly larvae is a promising biotechnology for waste reduction and control of antibiotic pollution. To determine how vermicomposting influences antibiotic resistance traits in swine manure, we explored the resistome and associated bacterial community dynamics during larvae gut transit over 6 days of treatment. In total, 94 out of 158 antibiotic resistance genes (ARGs) were significantly attenuated (by 85%), while 23 were significantly enriched (3.9-fold) following vermicomposting. The manure-borne bacterial community showed a decrease in the relative abundance of Bacteroidetes, and an increase in Proteobacteria, specifically Ignatzschineria, following gut transit. ARG attenuation was significantly correlated with changes in microbial community succession, especially reduction in Clostridiales and Bacteroidales. Six genomes were assembled from the manure, vermicompost (final product) and gut samples, including Pseudomonas, Providencia, Enterococcus, Bacteroides and Alcanivorax. Transposon-linked ARGs were more abundant in gut-associated bacteria compared with those from manure and vermicompost. Further, ARG-transposon gene cassettes had a high degree of synteny between metagenomic assemblies from gut and vermicompost samples, highlighting the significant contribution of gut microbiota through horizontal gene transfer to the resistome of vermicompost. In conclusion, the larvae gut microbiome significantly influences manure-borne community succession and the antibiotic resistome during animal manure processing.

Bacterial Associations Across House Fly Life History: Evidence for Transstadial Carriage From Managed Manure

House flies (Diptera: Muscidae; Musca domestica L.) associate with microbe-rich substrates throughout life history. Because larvae utilize bacteria as a food source, most taxa present in the larval substrate, e.g., manure, are digested or degraded. However, some species survive and are present as third-instar larvae begin pupation. During metamorphosis, many bacteria are again lost during histolysis of the larval gut and subsequent remodeling to produce the gut of the imago. It has been previously demonstrated that some bacterial species survive metamorphosis, being left behind in the puparium, present on the body surface, or in the gut of the emerged adult. We used a combined culture-molecular approach to identify viable microbes from managed manure residue and a wild population of house fly larvae, pupae, puparia, and adults to assess transstadial carriage. All larval (10/10), pupal (10/10), and puparial (10/10) cultures were positive for bacteria. Several bacterial species that were present in larvae also were present either in pupae or puparia. Four viable bacterial species were detectable in 6 of 10 imagoes reared from manure. Of note is the apparent transstadial carriage of Bacillus sonorensis, which has been associated with milk spoilage at dairies, and Alcaligenes faecalis, which can harbor numerous antibiotic resistance genes on farms. The potential of newly emerged flies to harbor and disseminate bacteria from managed manure on farms is an understudied risk that deserves further evaluation.

Attenuation of veterinary antibiotics in full-scale vermicomposting of swine manure via the housefly larvae (Musca domestica)

Animal waste from concentrated swine farms is widely considered to be a source of environmental pollution, and the introduction of veterinary antibiotics in animal manure to ecosystems is rapidly becoming a major public health concern. A housefly larvae (Musca domestica) vermireactor has been increasingly adopted for swine manure value-added bioconversion and pollution control, but few studies have investigated its efficiency on antibiotic attenuation during manure vermicomposting. In this study we explored the capacity and related attenuation mechanisms of antibiotic degradation and its linkage with waste reduction by field sampling during a typical cycle (6 days) of full-scale larvae manure vermicomposting. Nine antibiotics were dramatically removed during the 6-day vermicomposting process, including tetracyclines, sulfonamides, and fluoroquinolones. Of these, oxytetracycline and ciprofloxacin exhibited the greater reduction rate of 23.8 and 32.9 mg m⁻², respectively. Environmental temperature, pH, and total phosphorus were negatively linked to the level of residual antibiotics, while organic matter, total Kjeldahl nitrogen, microbial respiration intensity, and moisture exhibited a positive effect. Pyrosequencing data revealed that the dominant phyla related to Firmicutes, Bacteroidetes, and Proteobacteria accelerated manure biodegradation likely through enzyme catalytic reactions, which may enhance antibiotic attenuation during vermicomposting.

Acquisition and structuring of midgut bacterial communities in gypsy moth (Lepidoptera: Erebidae) larvae

Insects are associated with a diversity of bacteria that colonize their midguts. The extent to which these communities reflect maternal transmission, environmental acquisition, and subsequent structuring by the extreme conditions within the insect gut are poorly understood in many species. We used gypsy moth (Lymantria dispar L.) as a model to investigate interactions between egg mass and environmental sources of bacteria on larval midgut communities. Egg masses were collected from several wild and laboratory populations, and the effects of diet, initial egg mass community, and internal host environment were evaluated using 454 16S-rRNA gene pyrosequencing. Wild populations were highly diverse, while laboratory-maintained egg masses were associated with few operational taxonomic units. As larvae developed, their midgut bacterial communities became more similar to each other and the consumed diet despite initial differences in egg mass-associated bacteria. Subsequent experiments revealed that while midgut membership was more similar to bacteria associated with diet than with egg mass-associated bacteria, we were unable to detect distinct, persistent differences attributable to specific host plants. The differences between foliar communities and midgut communities of larvae that ingested them were owing to relative changes in populations of several bacteria phylotypes. We conclude that gypsy moth has a relatively characteristic midgut bacterial community that is reflective of, but ultimately distinct from, its foliar diet. This work demonstrates that environmental acquisition of diverse microbes can lead to similar midgut bacterial assemblages, underscoring the importance of host physiological environment in structuring bacterial communities.

Isolation and characterization of bacteria from midgut of the rice water weevil (Coleoptera: Curculionidae)

Gut bacteria are known to play important and often essential roles in the biology of insects. Theoretically, they can be genetically manipulated, then reintroduced into insects to negatively modify specific biological features. The weevil superfamily Curculionoidea is one of the most species-rich and successful animal groups on earth, but currently the overall knowledge of the bacterial communities in weevils and their associations with hosts is still limited. In this study, we isolated and characterized the bacteria in the midgut of an invasive weevil, Lissorhoptrus oryzophilus Kuschel, by culturing methods. Female adults of this weevil were collected from four different geographic regions of the United States and mainland China. Sequencing of the bacterial 16S rRNA amplicons demonstrated that the major culturable gut bacteria of rice water weevil are γ-proteobacteria and Bacilli. The gut bacterial composition differs among regions, with many of the bacteria isolated from only a single region while several were detected from more than one region. Overall, the diversity of gut bacteria in rice water weevil is relatively low. The possible origins of certain bacteria are discussed in relation to the weevil, rice plant, and bacteria.

Unearthing carrion beetles' microbiome: characterization of bacterial and fungal hindgut communities across the Silphidae

Carrion beetles (Coleoptera, Silphidae) are well known for their behaviour of exploiting vertebrate carcasses for nutrition. While species in the subfamily Silphinae feed on large carcasses and on larvae of competing scavengers, the Nicrophorinae are unique in monopolizing, burying and defending small carrion, and providing extensive biparental care. As a first step towards investigating whether microbial symbionts may aid in carcass utilization or defence, we characterized the microbial hindgut communities of six Nicrophorinae (Nicrophorus spp.) and two Silphinae species (Oiceoptoma noveboracense and Necrophila americana) by deep ribosomal RNA amplicon sequencing. Across all species, bacteria in the family Xanthomonadaceae, related to Ignatzschineriao larvae, were consistently common, and several other taxa were present in lower abundance (Enterobacteriales, Burkholderiales, Bacilli, Clostridiales and Bacteroidales). Additionally, the Nicrophorinae showed high numbers of unusual Clostridiales, while the Silphinae were characterized by Flavobacteriales and Rhizobiales (Bartonella sp.). In addition to the complex community of bacterial symbionts, each species of carrion beetle harboured a diversity of ascomycetous yeasts closely related to Yarrowia lipolytica. Despite the high degree of consistency in microbial communities across the Silphidae--specifically within the Nicrophorinae--both the fungal symbiont phylogeny and distance-based bacterial community clustering showed higher congruence with sampling locality than host phylogeny. Thus, despite the possibility for vertical transmission via anal secretions, the distinct hindgut microbiota of the Silphidae appears to be shaped by frequent horizontal exchange or environmental uptake of symbionts. The microbial community profiles, together with information on host ecology and the metabolic potential of related microorganisms, allow us to propose hypotheses on putative roles of the symbionts in carcass degradation, detoxification and defence.

Comparative evaluation of the gut microbiota associated with the below- and above-ground life stages (larvae and beetles) of the forest cockchafer, Melolontha hippocastani

A comparison of the diversity of bacterial communities in the larval midgut and adult gut of the European forest cockchafer (Melolontha hippocastani) was carried out using approaches that were both dependent on and independent of cultivation. Clone libraries of the 16S rRNA gene revealed 150 operational taxonomic units (OTUs) that belong to 11 taxonomical classes and two other groups that could be classified only to the phylum level. The most abundant classes were β, δ and γ-proteobacteria, Clostridia, Bacilli, Erysipelotrichi and Sphingobacteria. Although the insect’s gut is emptied in the prepupal stage and the beetle undergoes a long diapause period, a subset of eight taxonomic classes from the aforementioned eleven were found to be common in the guts of diapausing adults and the larval midguts (L2, L3). Moreover, several bacterial phylotypes belonging to these common bacterial classes were found to be shared by the larval midgut and the adult gut. Despite this, the adult gut bacterial community represented a subset of that found in the larvae midgut. Consequently, the midgut of the larval instars contains a more diverse bacterial community compared to the adult gut. On the other hand, after the bacteria present in the larvae were cultivated, eight bacterial species were isolated. Moreover, we found evidence of the active role of some of the bacterial species isolated in food digestion, namely, the presence of amylase and xylanolytic properties. Finally, fluorescence in situ hybridization allowed us to confirm the presence of selected species in the insect gut and through this, their ecological niche as well as the metagenomic results. The results presented here elucidated the heterogeneity of aerobic and facultative bacteria in the gut of a holometabolous insect species having two different feeding habits.

Do diet and taxonomy influence insect gut bacterial communities?

Many insects contain diverse gut microbial communities. While several studies have focused on a single or small group of species, comparative studies of phylogenetically diverse hosts can illuminate general patterns of host-microbiota associations. In this study, we tested the hypotheses that (i) host diet and (ii) host taxonomy structure intestinal bacterial community composition among insects. We used published 16S rRNA gene sequence data for 58 insect species in addition to four beetle species sampled from the Sevilleta National Wildlife Refuge to test these hypotheses. Overall, gut bacterial species richness in these insects was low. Decaying wood xylophagous insects harboured the richest bacterial gut flora (102.8 species level operational taxonomic units (OTUs)/sample ± 71.7, 11.8 ± 5.9 phylogenetic diversity (PD)/sample), while bees and wasps harboured the least rich bacterial communities (11.0 species level OTUs/sample ± 5.4, 2.6 ± 0.8 PD/sample). We found evidence to support our hypotheses that host diet and taxonomy structure insect gut bacterial communities (P < 0.001 for both). However, while host taxonomy was important in hymenopteran and termite gut community structure, diet was an important community structuring factor particularly for insect hosts that ingest lignocellulose-derived substances. Our analysis provides a baseline comparison of insect gut bacterial communities from which to test further hypotheses concerning proximate and ultimate causes of these associations.

Prevalence and relative risk of Cronobacter spp., Salmonella spp., and Listeria monocytogenes associated with the body surfaces and guts of individual filth flies

Although flies are important vectors of food-borne pathogens, there is little information to accurately assess the food-related health risk of the presence of individual flies, especially in urban areas. This study quantifies the prevalence and the relative risk of food-borne pathogens associated with the body surfaces and guts of individual wild flies. One hundred flies were collected from the dumpsters of 10 randomly selected urban restaurants. Flies were identified using taxonomic keys before being individually dissected. Cronobacter spp., Salmonella spp., and Listeria monocytogenes were detected using the PCR-based BAX system Q7. Positive samples were confirmed by culture on specific media and through PCR amplification and sequencing or ribotyping. Among collected flies were the housefly, Musca domestica (47%), the blowflies, Lucilia cuprina (33%) and Lucilia sericata (14%), and others (6%). Cronobacter species were detected in 14% of flies, including C. sakazakii, C. turicensis, and C. universalis, leading to the proposal of flies as a natural reservoir of this food-borne pathogen. Six percent of flies carried Salmonella enterica, including the serovars Poona, Hadar, Schwarzengrund, Senftenberg, and Brackenridge. L. monocytogenes was detected in 3% of flies. Overall, the prevalence of food-borne pathogens was three times greater in the guts than on the body surfaces of the flies. The relative risk of flies carrying any of the three pathogens was associated with the type of pathogen, the body part of the fly, and the ambient temperature. These data enhance the ability to predict the microbiological risk associated with the presence of individual flies in food and food facilities.

Swine manure vermicomposting via housefly larvae (Musca domestica): the dynamics of biochemical and microbial features

Improper handling of animal manure generated from concentrated swine operations greatly deteriorates water ecosystems. In this study, a full-scale vermireactor using housefly larvae (Musca domestica) was designed to investigate the effectiveness and efficiency of swine manure reduction, and to explore the associated biochemical-biological mechanisms. The one-week larvae vermireactor resulted in a total weight reduction rate of 106±17 kg/(m(3) d) and moisture reduction of 80.2%. Microbial activities in manure decreased by 45% after vermicomposting, while the activities of cellulose, proteases, and phosphatases in the vermicompost were significantly 69 times, 48%, and 82% lower than those in raw manure, respectively. The vermicompost was exclusively dominated by Entomoplasma somnilux, Proteobacterium, and Clostridiaceae bacterium where the microbial diversity was decreased from 2.57 in raw manure to 1.77. Correlation coefficients statistic showed that organic C might be a key indicator of the biochemical features and microbial functions of the larvae vermireactor.

Phylogenetic characterization of bacteria in the gut of house flies (Musca domestica L.)

House flies (Musca domestica L.) are cosmopolitan, ubiquitous, synanthropic insects that serve as mechanical or biological vectors for various microorganisms. To fully assess the role of house flies in the epidemiology of human diseases, it is essential to understand the diversity of microbiota harbored by natural fly populations. This study aimed to identify the diversity of house fly gut bacteria by both culture-dependent and culture-independent approaches. A total of 102 bacterial strains were isolated from the gut of 65 house flies collected from various public places including a garden, public park, garbage/dump area, public toilet, hospital, restaurant/canteen, mutton shop/market, and house/human habitation. Molecular phylogenetic analyses placed these isolates into 22 different genera. The majority of bacteria identified were known potential pathogens of the genera Klebsiella, Aeromonas, Shigella, Morganella, Providencia, and Staphylococcus. Culture-independent methods involved the construction of a 16S rRNA gene clone library, and sequence analyses supported culture recovery results. However, additional bacterial taxa not determined via culture recovery were revealed using this methodology and included members of the classes Alphaproteobacteria, Deltaproteobacteria, and the phylum Bacteroidetes. Here, we show that the house fly gut is an environmental reservoir for a vast number of bacterial species, which may have impacts on vector potential and pathogen transmission.