Core Gut Research Articles

The Core Gut Microbiome of the American Cockroach, Periplaneta americana, Is Stable and Resilient to Dietary Shifts.

The gut microbiome plays an important role in the overall health of its host. A healthy gut microbiota typically assists with defense against pathogens and the digestion and absorption of nutrients from food, while dysbiosis of the gut microbiota has been associated with reduced health. In this study, we examined the composition and stability of the gut microbiota from the omnivorous cockroach Periplaneta americana. We found that P. americana hosts a diverse core gut microbiome that remains stable after drastic long-term changes in diet. While other insects, notably ant and bee species, have evolved mechanisms for maintaining a stable association with specific gut microbiota, these insects typically host low-diversity gut microbiomes and consume specialized diets. In contrast, P. americana hosts a gut microbiota that is highly species rich and consumes a diverse solid diet, suggesting that cockroaches have evolved unique mechanisms for developing and maintaining a stable gut microbiota.

Microbial Community of Healthy Thai Vegetarians and Non-Vegetarians, Their Core Gut Microbiota, and Pathogen Risk.

Pyrosequencing analysis of intestinal microflora from healthy Thai vegetarians and non-vegetarians exhibited 893 OTUs covering 189 species. The strong species indicators of vegetarians and non-vegetarians were Prevotella copri and Bacteroides vulgatus as well as bacteria close to Escherichia hermanii with % relative abundance of 16.9 and 4.5-4.7, respectively. Core gut microbiota of the vegetarian and non-vegetarian groups consisted of 11 and 20 different bacterial species, respectively, belonging to Actinobacteria, Firmicutes, and Proteobacteria commonly found in both groups. Two species, Faecalibacterium prausnitzii and Gemmiger formicilis, had a prevalence of 100% in both groups. Three species, Clostridium nexile, Eubacterium eligens, and P. copri, showed up in most vegetarians, whereas more diversity of Collinsella aerofaciens, Ruminococcus torques, various species of Bacteroides, Parabacteroides, Escherichia, and different species of Clostridium and Eubacterium were found in most non-vegetarians. Considering the correlation of personal characters, consumption behavior, and microbial groups, the age of non-vegetarians showed a strong positive correlation coefficient of 0.54 (p = 0.001) to Bacteroides uniformis but exhibited a moderate one to Alistipes finegoldii and B. vulgatus. Only a positive moderate correlation of body mass index and Parabacteroides distasonis appeared. Based on the significant abundance of potential pathogens, the microbiota of the non-vegetarian group showed an abundance of potential pathogen varieties of Bilophila wadsworthia, Escherichia coli, and E. hermannii, whereas that of the vegetarian group served for only Klebsiella pneumoniae. These results implied that the microbiota of vegetarians with high abundance of P. copri and low potential pathogen variety would be a way to maintain good health in Thais.

BIODIVERSITY OF GUT MICROFLORA OF Oreochromis niloticus BASED ON CULTURE-INDEPENDENT rRNA GENE ANALYSES AT LAKE NASSER, EGYPT

The diversity of Oreochromis niloticus gut microbiome domains, eukaryotes, bacteria and archaea, was studied to understand the contribution of microbiota to the health of the fish. Fishes were collected from four different Khors, Kalabsha, Wadi Abyad, Tushka and Korosko, of Lake Nasser, Egypt. The approach of this study depends on culture-independent PCR/DGGE and sequence of small subunit of rRNA genes, 18S rRNA gene and 16S rRNA gene. The DGGE patterns displayed 5, 12 and 5 band groups, phylotypes, for eukaryotic 18S rRNA gene, bacterial and archaeal 16S rRNA genes, respectively, in gut contents from the studied khors. DGGE showed bands, which were common and specific for each site and could be used as a bar code to certify the origin of the fish. Statistical analyses, using binary matrix, showed numbers of DGGE bands, 1, 2 and 2, for eukaryotes, bacteria and archaea, respectively, were commonly occurred in all studied khors. The DGGE phylotype, 3.Euk.Kr characterized eukaryotes in Khor Korosko. Phylogenetic analyses showed that two of eukaryotic phylotypes, 1.Euk.Kl.Kr and 2.Euk.Common, were belonged to crustacean Ostracoda. Bacterial phylotypes in all studied khors were located in the branch of cyanobacteria, alpha proteobacteria, but most of them constituted unique phylogenetic lineages within the branch of uncultured environmental bacteria. All archaeal phylotypes were located in the branch of methanogenic uncultured euryarchaeota. Some helminthes, of the genera Neoechinorhynchus and Catenula, -like rRNA gene phylotypes were recorded in guts from Kalabsha, Tushka and Korosko, suggesting common gut parasitic worms. The DGGE patterns and sequence analyses showed high similarities of eukaryote, bacteria and archaea rRNA gene phylotype compositions in fish guts from distant khors, implicating core gut microbiome. This is the first survey of all microbiome domains in tilapia guts at Lake Nasser based on molecular approaches.

Microbial composition in different gut locations of weaning piglets receiving antibiotics.

ObjectiveThe aim of this study was to examine shifts in the composition of the bacterial population in the intestinal tracts (ITs) of weaning piglets by antibiotic treatment using high-throughput sequencing.MethodsSixty 28-d-old weaning piglets were randomly divided into two treatment groups. The Control group was treated with a basal diet without antibiotics. The Antibiotic group’s basal diet contained colistin sulfate at a concentration of 20 g per ton and bacitracin zinc at a concentration of 40 g per ton. All of the pigs were fed for 28 days. Then, three pigs were killed, and the luminal contents of the jejunum, ileum, cecum, and colon were collected for DNA extraction and high-throughput sequencing.ResultsThe results showed that the average daily weight gain of the antibiotic group was significantly greater (p<0.05), and the incidence of diarrhea lower (p>0.05), than the control group. A total of 812,607 valid reads were generated. Thirty-eight operational taxonomic units (OTUs) that were found in all of the samples were defined as core OTUs. Twenty-one phyla were identified, and approximately 90% of the classifiable sequences belonged to the phylum Firmicutes. Forty-two classes were identified. Of the 232 genera identified, nine genera were identified as the core gut microbiome because they existed in all of the tracts. The proportion of the nine core bacteria varied at the different tract sites. A heat map was used to understand how the numbers of the abundant genera shifted between the two treatment groups.ConclusionAt different tract sites the relative abundance of gut microbiota was different. Antibiotics could cause shifts in the microorganism composition and affect the composition of gut microbiota in the different tracts of weaning piglets.

A bacterial filter protects and structures the gut microbiome of an insect.

Associations with symbionts within the gut lumen of hosts are particularly prone to disruption due to the constant influx of ingested food and non-symbiotic microbes, yet we know little about how partner fidelity is maintained. Here we describe for the first time the existence of a gut morphological filter capable of protecting an animal gut microbiome from disruption. The proventriculus, a valve located between the crop and midgut of insects, functions as a micro-pore filter in the Sonoran Desert turtle ant (Cephalotes rohweri), blocking the entry of bacteria and particles ⩾0.2 μm into the midgut and hindgut while allowing passage of dissolved nutrients. Initial establishment of symbiotic gut bacteria occurs within the first few hours after pupation via oral–rectal trophallaxis, before the proventricular filter develops. Cephalotes ants are remarkable for having maintained a consistent core gut microbiome over evolutionary time and this partner fidelity is likely enabled by the proventricular filtering mechanism. In addition, the structure and function of the cephalotine proventriculus offers a new perspective on organismal resistance to pathogenic microbes, structuring of gut microbial communities, and development and maintenance of host–microbe fidelity both during the animal life cycle and over evolutionary time.

High-throughput sequencing reveals the core gut microbiome of Bar-headed goose (Anser indicus) in different wintering areas in Tibet.

Elucidating the spatial dynamic and core gut microbiome related to wild bar‐headed goose is of crucial importance for probiotics development that may meet the demands of bar‐headed goose artificial breeding industries and accelerate the domestication of this species. However, the core microbial communities in the wild bar‐headed geese remain totally unknown. Here, for the first time, we present a comprehensive survey of bar‐headed geese gut microbial communities by Illumina high‐throughput sequencing technology using nine individuals from three distinct wintering locations in Tibet. A total of 236,676 sequences were analyzed, and 607 OTUs were identified. We show that the gut microbial communities of bar‐headed geese have representatives of 14 phyla and are dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The additive abundance of these four most dominant phyla was above 96% across all the samples. At the genus level, the sequences represented 150 genera. A set of 19 genera were present in all samples and considered as core gut microbiome. The top seven most abundant core genera were distributed in that four dominant phyla. Among them, four genera (Lactococcus, Bacillus, Solibacillus, and Streptococcus) belonged to Firmicutes, while for other three phyla, each containing one genus, such as Proteobacteria (genus Pseudomonas), Actinobacteria (genus Arthrobacter), and Bacteroidetes (genus Bacteroides). This broad survey represents the most in‐depth assessment, to date, of the gut microbes that associated with bar‐headed geese. These data create a baseline for future bar‐headed goose microbiology research, and make an original contribution to probiotics development for bar‐headed goose artificial breeding industries.

Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments.

It is now well accepted that the gut microbiota contributes to our health. However, what determines the microbiota composition is still unclear. Whereas it might be expected that the intestinal niche would be dominant in shaping the microbiota, studies in vertebrates have repeatedly demonstrated dominant effects of external factors such as host diet and environmental microbial diversity. Hypothesizing that genetic variation may interfere with discerning contributions of host factors, we turned to Caenorhabditis elegans as a new model, offering the ability to work with genetically homogenous populations. Deep sequencing of 16S rDNA was used to characterize the (previously unknown) worm gut microbiota as assembled from diverse produce-enriched soil environments under laboratory conditions. Comparisons of worm microbiotas with those in their soil environment revealed that worm microbiotas resembled each other even when assembled from different microbial environments, and enabled defining a shared core gut microbiota. Community analyses indicated that species assortment in the worm gut was non-random and that assembly rules differed from those in their soil habitat, pointing at the importance of competitive interactions between gut-residing taxa. The data presented fills a gap in C. elegans biology. Furthermore, our results demonstrate a dominant contribution of the host niche in shaping the gut microbiota.

Ecological Succession in the Honey Bee Gut: Shift in Lactobacillus Strain Dominance During Early Adult Development

In many vertebrates, social interactions and nutrition can affect the colonization of gut symbionts across generations. In the highly social honey bee, it is unknown to what extent the hive environment and older worker individuals contribute to the generational transmission of core gut bacteria. We used high-throughput sequencing to investigate the effect of nest materials and social contact on the colonization and succession of core hindgut microbiota in workers. With only brief exposure to hive materials following natural eclosion, gut bacterial communities at 3 and 7days contained phylotypes typically found in the guts of mature adults regardless of treatment. Continuous exposure to nest materials or direct social interactions with mature adults did not affect the diversity or abundance of gut bacterial communities at the scale examined. Similarly, a common pollen supplement fed by beekeepers during pollen dearth had no effect. A consideration of unique OTUs revealed extensive microbial succession independent of treatment. The dominant Lactobacillus strain at 3days was largely replaced by a different strain at day 7, revealing the colonization signature of a pioneer species. Similar but less pronounced patterns were evident in less abundant OTU's, many of which may influence community succession via alteration of the gut environment. Our results indicate that the process of bacterial community colonization in the hindgut is resilient to changes in the nutritional, hive, and social environment. Greater taxonomic resolution is needed to accurately resolve questions of ecological succession and typical proportional variation within and between core members of the gut bacterial community.

Feeding on microbiomes: effects of detritivory on the taxonomic and phylogenetic bacterial composition of animal manures.

Earthworms play a key role in nutrient cycling by interacting with microorganisms thus accelerating organic matter turnover in soil systems. As detritivores, some earthworm types ingest and digest a mixture of dead organic matter and microorganisms, like animal manures (i.e. animal gut microbiomes). Here we described the earthworm cast microbiome and the role ingested bacteria play on its composition. We fed Eisenia andrei with cow, horse and pig manures and determined the taxonomic and phylogenetic composition of the these manures before and after passage through the earthworm gut. Earthworm cast microbiomes showed a smaller diversity than the manure they fed on. Manures strongly differed in their taxonomic and phylogenetic composition, but these differences were markedly reduced once transformed into earthworm cast microbiomes after passage through the earthworm gut. The core earthworm cast microbiome comprised 30 OTUs (2.6% of OTUs from cast samples), of which 10 are possibly native to the earthworm gut. Most of the core cast microbiome OTUs belonged to phyla Actinobacteria and Proteobacteria, as opposed to already described animal core gut microbiomes, which are composed mainly of Firmicutes and Bacteroidetes. Our results suggest that earthworms build up their cast microbiome by selecting from the pool of ingested bacteria.

Geriatric Respondents and Non-Respondents to Probiotic Intervention Can be Differentiated by Inherent Gut Microbiome Composition.

Probiotic interventions are known to have been shown to influence the composition of the intestinal microbiota in geriatrics. The growing concern is the apparent variation in response to identical strain dosage among human volunteers. One factor that governs this variation is the host gut microbiome. In this study, we attempted to define a core gut metagenome, which could act as a predisposition signature marker of inherent bacterial community that can help predict the success of a probiotic intervention. To characterize the geriatric gut microbiome, we designed primers targeting the 16S rRNA hypervariable region V2-V3 followed by semiconductor sequencing using Ion Torrent PGM. Among respondents and non-respondents, the chief genera of phylum Firmicutes that showed significant differences are Lactobacillus, Clostridium, Eubacterium, and Blautia (q < 0.002), while in the genera of phylum Proteobacteria included Shigella, Escherichia, Burkholderia and Camphylobacter (q < 0.002). We have identified potential microbial biomarkers and taxonomic patterns that correlate with a positive response to probiotic intervention in geriatric volunteers. Future work with larger cohorts of geriatrics with diverse dietary influences could reveal the potential of the signature patterns of microbiota for personalized nutrition.

Towards an integrated understanding of the consequences of fungus domestication on the fungus-growing termite gut microbiota.

Approximately 30 million years ago (MYA), the subfamily of higher termites Macrotermitinae domesticated a fungus, Termitomyces, as the main plant decomposer and food source for the termite host. The origin of fungiculture shifted the composition of the termite gut microbiota, and some of the functional implications of this shift have recently been established. I review reports on the composition of the Macrotermitinae gut microbiota, evidence for a subfamily core gut microbiota, and the first insight into functional complementarity between fungal and gut symbionts. In addition, I argue that we need to explore the capacities of all members of the symbiotic communities, including better solidifying Termitomyces role(s) in order to understand putative complementary gut bacterial contributions. Approaches that integrate natural history and sequencing data to elucidate symbiont functions will be powerful, particularly if executed in comparative analyses across the well-established congruent termite-fungus phylogenies. This will allow for testing if gut communities have evolved in parallel with their hosts, with implications for our general understanding of the evolution of gut symbiont communities with hosts.

Comparison of the gut microbiomes of 12 bony fish and 3 shark species

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 518:209-223 (2015) - DOI: https://doi.org/10.3354/meps11034 Comparison of the gut microbiomes of 12 bony fish and 3 shark species Carrie E. Givens1,2, Briana Ransom1,3, Nasreen Bano1,4, James T. Hollibaugh1,* 1Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA 2Present address: US Geological Survey Michigan Water Science Center, 6520 Mercantile Way, Lansing, MI 48911, USA 3Present address: Oglethorpe County High School, 749 Athens Rd, Lexington, GA 30648, USA 4Present address: USDA ARS, 950 College Station Rd, Athens, GA 30605, USA *Corresponding author: aquadoc@uga.edu ABSTRACT: We used massively parallel sequencing (pyrosequencing) of 16S rRNA genes to compare the composition of microbial communities in the guts of 12 bony fish and 3 shark species. The species analyzed encompass herbivores and carnivores with varied digestive physiologies, are classified as pelagic and demersal species, and reside in estuarine to marine environments. We also compared the gut microbial assemblages of wild and cultured Fundulus heteroclitus and of juvenile and adult Lagodon rhomboides. A total of 1214355 sequences were filtered, denoised, trimmed, and then sorted into operational taxonomic units (OTUs) based on 97% sequence similarity. Bacteria representing 17 phyla were found among the sampled fish, with most fish hosting between 7 and 15 phyla. Proteobacteria OTUs were present in all fish and often dominated the libraries (3.0 to 98%; average: 61%). Firmicutes were also prevalent, but at a lower relative abundance, ranging between 1.3 and 45% (average: 17%). In most cases, the gut microflora of individual fish of a given species contained many of the same OTUs; however, some species (e.g. great barracuda) shared few OTUs among the individuals sampled. Although no single OTU was shared among all fish species, many of the OTUs present in one species’ core group were also found in the core groups of other species. Several OTUs were consistently found in the guts of multiple species, suggesting that these OTUs may be important contributors to fish gut functions such as digestion, nutrient absorption, and immune response. KEY WORDS: Fish gut · Gut microbiome · 16S rRNA · Gut microflora · 454-pyrosequencing · Shark gut · Core gut microbiome Full text in pdf format Supplementary material PreviousNextCite this article as: Givens CE, Ransom B, Bano N, Hollibaugh JT (2015) Comparison of the gut microbiomes of 12 bony fish and 3 shark species. Mar Ecol Prog Ser 518:209-223. https://doi.org/10.3354/meps11034 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 518. Online publication date: January 07, 2015 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2015 Inter-Research.

How informative is the mouse for human gut microbiota research?

The microbiota of the human gut is gaining broad attention owing to its association with a wide range of diseases, ranging from metabolic disorders (e.g. obesity and type 2 diabetes) to autoimmune diseases (such as inflammatory bowel disease and type 1 diabetes), cancer and even neurodevelopmental disorders (e.g. autism). Having been increasingly used in biomedical research, mice have become the model of choice for most studies in this emerging field. Mouse models allow perturbations in gut microbiota to be studied in a controlled experimental setup, and thus help in assessing causality of the complex host-microbiota interactions and in developing mechanistic hypotheses. However, pitfalls should be considered when translating gut microbiome research results from mouse models to humans. In this Special Article, we discuss the intrinsic similarities and differences that exist between the two systems, and compare the human and murine core gut microbiota based on a meta-analysis of currently available datasets. Finally, we discuss the external factors that influence the capability of mouse models to recapitulate the gut microbiota shifts associated with human diseases, and investigate which alternative model systems exist for gut microbiota research.

Investigating the long-term effect of subchronic phencyclidine-treatment on novel object recognition and the association between the gut microbiota and behavior in the animal model of schizophrenia

Subchronic phencyclidine (subPCP) treatment induces schizophrenic-like behavior in rodents, including cognitive deficits and increased locomotor sensitivity towards acute administration of PCP. Evidence is accumulating that the gut microbiota (GM) influences behavior through modulation of the microbiota–gut–brain axis, and hence, part of the variation within this animal model may derive from variation in the GM. The aims of this study was to investigate first, the duration of subPCP-induced cognitive impairment in the novel object recognition test, and second, the possible effect of subchronic PCP-treatment on the GM, and the association between the GM and the behavioral parameters. The association was further investigated by antibiotic reduction of the GM. Male Lister Hooded rats were dosed twice daily i.p. with either 5mg/kg PCP or sterile isotonic saline for seven days followed by a seven-day washout period. Rats were tested in the novel object recognition and the locomotor activity assays immediately after, three weeks after, or six weeks after washout, and the fecal GM was analyzed by high throughput sequencing. Antibiotic- and control-treated rats were tested in the same manner following washout. In conclusion, subPCP-treatment impaired novel object recognition up to three weeks after washout, whereas locomotor sensitivity was increased for at least six weeks after washout. Differences in the core gut microbiome immediately after washout suggested subPCP treatment to alter the GM. GM profiles correlated to memory performance. Administration of ampicillin abolished the subPCP-induced memory deficit. It thus seems reasonable to speculate that the GM influences memory performance, contributing to variation within the model.

Marek's disease virus influences the core gut microbiome of the chicken during the early and late phases of viral replication.

Marek's disease (MD) is an important neoplastic disease of chickens caused by the Marek's disease virus (MDV), an oncogenic alphaherpesvirus. In this study, dysbiosis induced by MDV on the core gut flora of chicken was assessed using next generation sequence (NGS) analysis. Total fecal and cecum-derived samples from individual birds were used to estimate the influence of MDV infection on the gut microbiome of chicken. Our analysis shows that MDV infection alters the core gut flora in the total fecal samples relatively early after infection (2-7 days) and in the late phase of viral infection (28-35 days) in cecal samples, corresponding well with the life cycle of MDV. Principle component analyses of total fecal and cecal samples showed clustering at the early and late time points, respectively. The genus Lactobacillus was exclusively present in the infected samples in both total fecal and cecal bird samples. The community colonization of core gut flora was altered by viral infection, which manifested in the enrichment of several genera during the early and late phases of MDV replication. The results suggest a relationship between viral infection and microbial composition of the intestinal tract that may influence inflammation and immunosuppression of T and B cells in the host.

Mongolians core gut microbiota and its correlation with seasonal dietary changes.

Historically, the Mongol Empire ranks among the world's largest contiguous empires, and the Mongolians developed their unique lifestyle and diet over thousands of years. In this study, the intestinal microbiota of Mongolians residing in Ulan Bator, TUW province and the Khentii pasturing area were studied using 454 pyrosequencing and q-PCR technology. We explored the impacts of lifestyle and seasonal dietary changes on the Mongolians' gut microbes. At the phylum level, the Mongolians's gut populations were marked by a dominance of Bacteroidetes (55.56%) and a low Firmicutes to Bacteroidetes ratio (0.71). Analysis based on the operational taxonomic unit (OTU) level revealed that the Mongolian core intestinal microbiota comprised the genera Prevotella, Bacteroides, Faecalibacterium, Ruminococcus, Subdoligranulum and Coprococcus. Urbanisation and life-style may have modified the compositions of the gut microbiota of Mongolians from Ulan Bator, TUW and Khentii. Based on a food frequency questionnaire, we found that the dietary structure was diverse and stable throughout the year in Ulan Bator and TUW, but was simple and varied during the year in Khentii. Accordingly, seasonal effects on intestinal microbiota were more distinct in Khentii residents than in TUW or Ulan Bator residents.

Program and AbstractsThirty-fourth Annual Meeting of the Surgical Infection SocietyBaltimore, MarylandMay 1–3, 2014

Program and AbstractsThirty-fourth Annual Meeting of the Surgical Infection SocietyBaltimore, MarylandMay 1–3, 2014

The Intestinal Metabolome: An Intersection Between Microbiota and Host

Recent advances that allow us to collect more data on DNA sequences and metabolites have increased our understanding of connections between the intestinal microbiota and metabolites at a whole-systems level. We can also now better study the effects of specific microbes on specific metabolites. Here, we review how the microbiota determines levels of specific metabolites, how the metabolite profile develops in infants, and prospects for assessing a person's physiological state based on their microbes and/or metabolites. Although data acquisition technologies have improved, the computational challenges in integrating data from multiple levels remain formidable; developments in this area will significantly improve our ability to interpret current and future data sets.

Pyrotag Sequencing of the Gut Microbiota of the Cockroach Shelfordella lateralis Reveals a Highly Dynamic Core but Only Limited Effects of Diet on Community Structure

Although blattid cockroaches and termites share a common ancestor, their diets are distinctly different. While termites consume a highly specialized diet of lignocellulose, cockroaches are omnivorous and opportunistic feeders. The role of the termite gut microbiota has been studied intensively, but little is known about the cockroach gut microbiota and its function in digestion and nutrition, particularly the adaptation to different diets. Our analyses of the bacterial gut microbiota of the blattid cockroach Shelfordella lateralis combining terminal restriction fragment length polymorphism of their 16S rRNA genes with physiological parameters (microbial metabolites, hydrogen and methane emission) indicated substantial variation between individuals but failed to identify any diet-related response. Subsequent deep-sequencing of the 16S rRNA genes of the colonic gut microbiota of S. lateralis fed either a high- or a low-fiber diet confirmed the absence of bacterial taxa that responded to diet. Instead, we found a small number of abundant phylotypes that were consistently present in all samples and made up half of the community in both diet groups. They varied strongly in abundance between individual samples at the genus but not at the family level. The remaining phylotypes were inconsistently present among replicate batches. Our findings suggest that S. lateralis harbors a highly dynamic core gut microbiota that is maintained even after fundamental dietary shifts, and that any dietary effects on the gut community are likely to be masked by strong individual variations.

Microbial gut diversity of Africanized and European honey bee larval instars.

The first step in understanding gut microbial ecology is determining the presence and potential niche breadth of associated microbes. While the core gut bacteria of adult honey bees is becoming increasingly apparent, there is very little and inconsistent information concerning symbiotic bacterial communities in honey bee larvae. The larval gut is the target of highly pathogenic bacteria and fungi, highlighting the need to understand interactions between typical larval gut flora, nutrition and disease progression. Here we show that the larval gut is colonized by a handful of bacterial groups previously described from guts of adult honey bees or other pollinators. First and second larval instars contained almost exclusively Alpha 2.2, a core Acetobacteraceae, while later instars were dominated by one of two very different Lactobacillus spp., depending on the sampled site. Royal jelly inhibition assays revealed that of seven bacteria occurring in larvae, only one Neisseriaceae and one Lactobacillus sp. were inhibited. We found both core and environmentally vectored bacteria with putatively beneficial functions. Our results suggest that early inoculation by Acetobacteraceae may be important for microbial succession in larvae. This assay is a starting point for more sophisticated in vitro models of nutrition and disease resistance in honey bee larvae.