Core Bacterial Community Research Articles

Bacterial Communities of House Flies from Beef and Dairy Cattle Operations are Diverse and Contain Pathogens of Medical and Veterinary Importance.

Adult house flies (Musca domestica L.) are important reservoirs and mechanical vectors of bacteria in livestock operations. House fly bacterial communities are influenced by their local environment, yet a comprehensive understanding of bacterial diversity, pathogen prevalence, and bacterial source is not fully understood. We characterized bacterial communities from adult female house flies and associated manure samples from beef and dairy cattle farms in Kansas, Oklahoma, and Texas over four months (July-October). Bacterial community composition in flies and manure reflected the local environment, and house flies shared the majority (≥ 99%) of bacterial taxa with manure. The variability of bacterial diversity was greater among individual fly (species richness range: 48-1747) samples than manure (species richness range: 345-1162). Temporal variability of fly bacterial diversity was observed within each farm type. Bacterial taxa of veterinary and medical importance such as Corynebacterium, Turicibacter, Staphylococcus, Streptococcus, and Acinetobacter were highly prevalent in flies, constituting core bacterial communities. The prevalence of bacterial taxa associated with bovine keratoconjunctivitis (IBK) and bovine respiratory disease (BRD) was higher in flies than in manure and prevalence varied monthly. This study underscores the crucial role house flies play as carriers of cattle pathogens, contributing to their dissemination among animals and to off-site locations, where they pose a threat to surrounding communities and agricultural operations.

Succession from acetoclastic to hydrogenotrophic microbial community during sewage sludge anaerobic digestion for bioenergy production.

To assess microbial dynamics during anaerobic digestion (AD) of sewage sludge (SWS) from a municipal Wastewater Treatment Plant (WWTP), a Biochemical Methane Potential (BMP) assay at 37°C under mono-digestion conditions was conducted. Utilizing the Illumina MiSeq platform, 16S ribosomal RNA (rRNA) gene sequencing unveiled a core bacterial community in the solid material, showcasing notable variations in profiles. The research investigates changes in microbial communities and metabolic pathways to understand their impact on the efficiency of the digestion process. Prior to AD, the relative abundance in SWS was as follows: Proteobacteria > Bacteroidota > Actinobacteriota. Post-AD, the relative abundance shifted to Firmicutes > Synergistota > Proteobacteria, with Sporanaerobacter and Clostridium emerging as dominant genera. Notably, the methanogenic community underwent a metabolic pathway shift from acetoclastic to hydrogenotrophic in the lab-scale reactors. At the genus level, Methanosaeta, Methanolinea, and Methanofastidiosum predominated initially, while post-AD, Methanobacterium, Methanosaeta, and Methanospirillum took precedence. This metabolic transition may be linked to the increased abundance of Firmicutes, particularly Clostridia, which harbor acetate-oxidizing bacteria facilitating the conversion of acetate to hydrogen.

Effects of Formulated Pellet Feed or Live Fish Food on the Intestinal and Aquaculture Water Microbial Communities in Goldfish, Carassius auratus

This study investigates the impact of different diets on fish growth and bacterial community structure present in the intestine of goldfish (Carassius auratus) and their aquaculture water under recirculating water conditions. We assumed that different types of diet would form different intestinal microbiota that may affect host growth. Using Illumina MiSeq high-throughput sequencing, we analyzed bacterial communities in goldfish fed with formulated pellet feed, Tubifex worms (Limnodrilus hoffmeisteri), and an alternating diet of both. Over a 14-day feeding trial, no significant differences in juvenile goldfish growth were observed between groups. After 7 days, diet changes significantly influenced the abundance and diversity of intestinal bacteria, with the alternating diet notably enhancing bacterial diversity in both the intestines and water. However, these differences in bacterial diversity decreased by day 14. The results indicate that diet type affects microbial community diversity in the intestines and water of goldfish, and that goldfish intestines maintain a stable core bacterial community structure. This highlights the potential for optimizing diet types to enhance microbial health and stability in aquaculture systems and, in addition, provides an important scientific basis for alternative diets in goldfish aquaculture in the industry.

Abiotic stress reorganizes rhizosphere and endosphere network structure of Sorghum bicolor

Sorghum bicolor is a promising bioenergy feedstock with high biomass production and unusual tolerance for stresses such as water and nutrient limitation. While the membership of the sorghum microbiome in response to stress has been explored, relatively little is known about how microbe-microbe networks change under water- or nutrient-limited conditions. This is important because network changes can indicate impacts on the functionality and stability of microbial communities. We performed network-based analysis on the core bacterial and archaeal community of an agronomically promising high biomass bioenergy genotype, Grassl, grown under nitrogen and water stress. Stress caused relatively minor changes in bacterial abundances within soil, rhizosphere, and endosphere communities, but led to significant changes in bacterial network structure and modularity. We found a complete reorganization of network roles in all plant compartments as well as an increase in the modularity and proportion of positive associations which potentially could represent coexistence and cooperation in the sorghum bacterial/archaeal community under stress. While stressors are often believed to be destabilizing, we found stressed networks were as or more stable than non-stressed networks likely due to their redundancy and compartmentalization. Together, these findings support the idea that both sorghum and its bacterial/archaeal community can be resilient to future environmental stressors.

Compositional and functional succession of soil bacterial communities during long-term rice cultivation on saline-alkali soils: Insights derived from a new perspective of the core bacterial taxa

The conversion of saline-alkali soils into paddy fields for long-term rice cultivation involves multiple disturbances, and as a result, soil microbial communities are altered to adapt to a changing environment. A comprehensive understanding of the succession of soil bacterial communities that occurs during this process, however, is still lacking. In the present study, we utilized data obtained from rice paddies of different cultivation years to investigate the compositional and functional succession of the soil bacterial community. We focused on core bacterial taxa that were specifically enriched at different successional stages. Generalized joint attribute modeling (GJAM) was used to identify core bacterial taxa. Results indicated that bare saline-alkali soils shared few core amplicon sequence variants (ASVs) with paddy fields. Longimicrobiaceae from the phylum Gemmatimonadetes was dominant in bare saline-alkali soils, while their dominance was subsequently replaced by Burkholderiaceae and Pedosphaeraceae, phyla affiliated with the Proteobacteria and Verrucomicrobia, after 5 years and 23 years of rice cultivation, respectively. The abundance of nitrogen metabolism functions in the core bacterial community present in bare saline-alkali soils were higher than they were in other successional stages, while sulfur metabolism functions exhibited the opposite trend. These data indicate that the role of the core bacterial taxa in mediating nutrient cycling also changed and adapted to changing soil conditions as rice cultivation became established. Redundancy analysis (RDA) indicated that the compositions of the core bacterial community in Y0, Y5s, Y10s, and Y20s groups were driven by nitrate-nitrogen content, soil pH, available phosphorus content, and the ratio of total carbon to total nitrogen, respectively. In summary, the present study provides insights into the succession of soil bacterial communities and core bacterial taxa that occur during long-term rice cultivation.

Deciphering the environmental adaptation and functional trait of core and noncore bacterial communities in impacted coral reef seawater

Microorganisms play pivotal roles in different biogeochemical cycles within coral reef waters. Nevertheless, our comprehension of the microbially mediated processes following environmental perturbation is still limited. To gain a deeper insight into the environmental adaptation and nutrient cycling, particularly within core and noncore bacterial communities, it is crucial to understand reef ecosystem functioning. In this study, we delved into the microbial community structure and function of seawater in a coral reef under different degrees of anthropogenic disturbance. To achieve this, we harnessed the power of 16S rRNA gene high-throughput sequencing and metagenomics techniques. The results showed that a continuous temporal succession but little spatial heterogeneity in the bacterial communities of core and noncore taxa and functional profiles involved in nitrogen (N) and phosphorus (P) cycling. Eutrophication state (i.e., nutrient concentration and turbidity) and temperature played pivotal roles in shaping both the microbial community composition and functional traits of coral reef seawater. Within this context, the core subcommunity exhibited a remarkably broader habitat niche breadth, stronger phylogenetic signal and lower environmental sensitivity when compared to the noncore taxa. Null model analysis further revealed that the core subcommunity was governed primarily by stochastic processes, while deterministic processes played a more significant role in shaping the noncore subcommunity. Furthermore, our observations indicated that changes in function related to N cycling were correlated to the variations in noncore taxa, while core taxa played a more substantial role in critical processes such as P cycling. Collectively, these findings facilitated our knowledge about environmental adaptability of core and noncore bacterial taxa and shed light on their respective roles in maintaining diverse nutrient cycling within coral reef ecosystems.

Core bacterial communities dominated Purus frumentum biomass under different green manure returning amounts in saline-alkali soil

Core bacterial communities dominated Purus frumentum biomass under different green manure returning amounts in saline-alkali soil

Root rot induces a core assemblage of bacterial microbiome to prevent disease infection in Sanqi ginseng

Plants rely on rhizosphere microbes as the first line of defense against pathogen invasion and for maintaining the health of itself. Increasing evidence suggests that plants recruit beneficial microbes to the roots, strengthening their resistance to pathogens. However, the response of the rhizosphere core bacterial microbiome to root rot infection remains largely unclear. In this study, we investigated the rhizosphere and bulk soil core bacterial microbiome of healthy and root rot-diseased Sanqi ginseng in genuine production areas in China. We utilized 16S amplicon sequencing, co-occurrence network analysis, and strain culture approaches to explore whether root rot-induced plant rhizosphere alterations in the bacterial core microbiome could improve disease suppression. Root rot infection had a significant impact on the rhizosphere core bacterial microbiome of Sanqi ginseng. Root rot led to a reduction in the diversity and evenness of the core bacterial microbiome in the rhizosphere, while the variability of the core bacterial community in the rhizosphere increased. In response to fungal root rot pathogen infestation, Sanqi ginseng recruited potentially beneficial bacteria with disease-suppressive functions to the rhizosphere, such as Sphingobium, Pseudoxanthomonas, Pseudomonas, Stenotrophomonas, and Flavobacterium. Function prediction analysis demonstrated a remarkable enrichment of several functional genes involved in antibiotic biosynthesis in the rhizosphere that was infected with root rot. Strain isolation and pot addition experiments further confirmed the effectiveness of root rot rhizosphere-specific enrichment of Operational Taxonomic Units (OTUs) for controlling root rot. Furthermore, co-occurrence network analysis indicated that root rot activated the disease-suppressive functions of the rhizosphere core bacterial microbiome by enhancing complexity and connectivity at the expense of network stability. These findings expand our knowledge of plant-microbe interactions and provides new evidence supporting the “cry for help” strategy for rhizosphere responses to root rot.

Novel insights into the synergetic degradation of pyrene by microbial communities from mangroves in China

Pyrene is a high molecular weight polycyclic aromatic hydrocarbon (HMW-PAHs). It is a ubiquitous, persistent, and carcinogenic environmental contaminant that has raised concern worldwide. This research explored synergistic bacterial communities for efficient pyrene degradation in seven typical Southern China mangroves. The bacterial communities of seven typical mangroves were enriched by pyrene, and enriched bacterial communities showed an excellent pyrene degradation capacity of > 95% (except for HK mangrove and ZJ mangrove). Devosia, Hyphomicrobium, Flavobacterium, Marinobacter, Algoriphahus, and Youhaiella all have significant positive correlations with pyrene (R>0, p < 0.05) by 16SrRNA gene sequencing and metagenomics analysis, indicated that these genera play a vital role in pyrene metabolism. Meanwhile, the functional genes were involved in pyrene degradation that was enriched in the bacterial communities, including the genes of nagAa, ndoR, pcaG, etc. Furthermore, the analyses of functional genes and binning genomes demonstrated that some bacterial communities as a unique teamwork to cooperatively participate in pyrene degradation. Interestingly, the genes related to biogeochemical cycles were enriched, such as narG , soxA, and cyxJ, suggested that bacterial communities were also helpful in maintaining the stability of the ecological environment. In addition, some novel species with pyrene-degradation potential were identified in the pyrene-degrading bacterial communities, which can enrich the resource pool of pyrene-degrading strains. Overall, this study will help develop further research strategies for pollutant removal.

Deciphering the core bacterial community structure and function and their response to environmental factors in activated sludge from pharmaceutical wastewater treatment plants

Pharmaceutical wastewater is recognized for its heightened concentrations of organic pollutants, and biological treatment stands out as an effective technology to remove these organic pollution. Therefore, a comprehensive exploration of core bacterial community compositions, functions, and their responses to environmental factors in pharmaceutical wastewater treatment plants (PWWTPs) is important for understanding the removal mechanism of these organic pollutants. This study comprehensively investigated 36 activated sludge (AS) samples from 15 PWWTPs in China. The results revealed that Proteobacteria (45.41%) was the dominant phylum in AS samples, followed by Bacteroidetes (19.54%) and Chloroflexi (4.13%). While the dominant genera were similar in both aerobic and anaerobic treatment processes, their relative abundances exhibited significant variations. Genera like HA73, Kosmotoga, and Desulfovibrio were more abundant during anaerobic treatment, while Rhodoplanes, Bdellovibrio, and Hyphomicrobium dominated during aerobic treatment. 13 and 10 core operational taxonomic units (OTUs) were identified in aerobic and anaerobic sludge, respectively. Further analysis revealed that core OTUs belonging to genera Kosmotoga, Desulfovibrio, Thauera, Hyphomicrobium, and Chelativorans, were associated with key functions, including sulfur metabolism, methane metabolism, amino acid metabolism, carbohydrate metabolism, toluene degradation, and nitrogen metabolism. Furthermore, this study highlighted the crucial roles of environmental factors, such as COD, NH4+-N, SO42−, and TP, in shaping both the structure and core functions of bacterial communities within AS of PWWTPs. Notably, these factors indirectly affect functional attributes by modulating the bacterial community composition and structure in pharmaceutical wastewater. These findings provide valuable insights for optimizing the efficiency of biochemical treatment processes in PWWTPs.

Impacts of humic substances, elevated temperature, and UVB radiation on bacterial communities of the marine sponge Chondrilla sp.

Sponges are abundant components of coral reefs known for their filtration capabilities and intricate interactions with microbes. They play a crucial role in maintaining the ecological balance of coral reefs. Humic substances (HS) affect bacterial communities across terrestrial, freshwater, and marine ecosystems. However, the specific effects of HS on sponge-associated microbial symbionts have largely been neglected. Here, we used a randomized-controlled microcosm setup to investigate the independent and interactive effects of HS, elevated temperature, and UVB radiation on bacterial communities associated with the sponge Chondrilla sp. Our results indicated the presence of a core bacterial community consisting of relatively abundant members, apparently resilient to the tested environmental perturbations, alongside a variable bacterial community. Elevated temperature positively affected the relative abundances of ASVs related to Planctomycetales and members of the families Pseudohongiellaceae and Hyphomonadaceae. HS increased the relative abundances of several ASVs potentially involved in recalcitrant organic matter degradation (e.g., the BD2-11 terrestrial group, Saccharimonadales, and SAR202 clade). There was no significant independent effect of UVB and there were no significant interactive effects of HS, heat, and UVB on bacterial diversity and composition. The significant, independent impact of HS on the composition of sponge bacterial communities suggests that alterations to HS inputs may have cascading effects on adjacent marine ecosystems.

Bioturbation effect of artificial inoculation on the flavor metabolites and bacterial communities in the Chinese Mao-tofu fermentation

A comparison between artificially inoculated Mao-tofu (CC) and naturally fermented Mao-tofu (MM) indicated that artificially adding Mucor plasmaticus to Mao-tofu dramatically enhanced the essential amino acid (EAA) content, as well as umami and sweet amino acids. Gas chromatography-tandem mass spectrometry (GC–MS/MS) analysis revealed that phenol (3.226 μg/g), 1-octen-3-ol (5.031 μg/g), ethyl heptanoate (1.646 μg/g), and indole (3.422 μg/g) were the key flavor components in Mao-tofu. Unlike MM, CC displayed a substantial increase in esters and a considerable decrease in foul odor substances, including sulfur-containing compounds and indole. Lactococcus raffinolactis, Enterobacter sp. 638, and Streptococcus parauberis KCTC 11537 represented the key bacterial species altering the amino acids and flavor of Mao-tofu according to PacBio single-molecule real-time (SMRT) sequencing and correlation analysis. This study presents the technical feasibility of artificially inoculating Mao-tofu to regulate the core bacterial communities and control the quality of fermented soybean products.

Deciphering the microbial landscapes in the early life stages of a high-value marine fish, cobia (Rachycentron canadum, Rachycentridae) through high-resolution profiling by PacBio SMRT sequencing

Microbial dynamics across multiple ontogenetic stages represent one confounding feature in teleost microbiome research. The present study recorded the dynamics in the whole microbiome of early life stages and the juvenile gut microbiome of a high-value mariculture species, cobia (Rachycentron canadum), during standard culturing practices. This is the first report on using the PacBio system targeting full-length 16S rRNA sequences, for deciphering fish microbiomes. The results highlighted a temporal shift in the whole microbiome compositions along the host's ontogenetic development. There was a significant decrease in Cyanobacteria and Firmicutes to Bacteroidetes ratio with a corresponding increase in Plactomycetacea and Bacteriodata in the whole microbiome profiles of the post-metamorphosis samples. The gut microbiome data suggested an adaptive mechanism toward establishing beneficial strains (Bacilli and Actinobacteria) alongside the ontogenetic progression. Nevertheless, a small, abundant core bacterial community occupied ∼50% and ∼ 64% of total abundance in the whole microbiome and gut microbiome, respectively. The results revealed high-dimensional microbial biomarkers for various ontogenetic stages of cobia during standard culturing practices. The composite dataset generated offers several possible sustainable means of microbiome manipulations to improve the low survival encountered in the early life stages of cobia.

Associated bacterial communities, confrontation studies, and comparative genomics reveal important interactions between Morchella with Pseudomonas spp.

Members of the fungal genus Morchella are widely known for their important ecological roles and significant economic value. In this study, we used amplicon and genome sequencing to characterize bacterial communities associated with sexual fruiting bodies from wild specimens, as well as vegetative mycelium and sclerotia obtained from Morchella isolates grown in vitro. These investigations included diverse representatives from both Elata and Esculenta Morchella clades. Unique bacterial community compositions were observed across the various structures examined, both within and across individual Morchella isolates or specimens. However, specific bacterial taxa were frequently detected in association with certain structures, providing support for an associated core bacterial community. Bacteria from the genus Pseudomonas and Ralstonia constituted the core bacterial associates of Morchella mycelia and sclerotia, while other genera (e.g., Pedobacter spp., Deviosa spp., and Bradyrhizobium spp.) constituted the core bacterial community of fruiting bodies. Furthermore, the importance of Pseudomonas as a key member of the bacteriome was supported by the isolation of several Pseudomonas strains from mycelia during in vitro cultivation. Four of the six mycelial-derived Pseudomonas isolates shared 16S rDNA sequence identity with amplicon sequences recovered directly from the examined fungal structures. Distinct interaction phenotypes (antagonistic or neutral) were observed in confrontation assays between these bacteria and various Morchella isolates. Genome sequences obtained from these Pseudomonas isolates revealed intriguing differences in gene content and annotated functions, specifically with respect to toxin-antitoxin systems, cell adhesion, chitinases, and insecticidal toxins. These genetic differences correlated with the interaction phenotypes. This study provides evidence that Pseudomonas spp. are frequently associated with Morchella and these associations may greatly impact fungal physiology.

Microbiota and Nutrient Portraits of European Roe Deer (Capreolus capreolus) Rumen Contents in Characteristic Southern German Habitats

Roe deer (Capreolus capreolus) are found in various habitats, from pure forest cultures to agricultural areas and mountains. In adapting to the geographically and seasonally differentiating food supply, they depend, above all, on an adapted microbiome. However, knowledge about the microbiome of wild ruminants still needs to be improved. There are only a few publications for individual species with a low number of samples. This study aims to identify a core microbiota for Bavarian roe deer and present nutrient and microbiota portraits of the individual habitat types. This study investigated the roe deer’s rumen (reticulorumen) content from seven different characteristic Bavarian habitat types. The focus was on the composition of nutrients, fermentation products, and the rumen bacterial community. A total of 311 roe deer samples were analysed, with the most even possible distribution per habitat, season, age class, and gender. Significant differences in nutrient concentrations and microbial composition were identified for the factors habitat, season, and age class. The highest crude protein content (plant protein and microbial) in the rumen was determined in the purely agricultural habitat (AG), the highest value of non-fibre carbohydrates in the alpine mountain forest, and the highest fibre content (neutral detergent fibre, NDF) in the pine forest habitat. Maximum values for fibre content go up to 70% NDF. The proportion of metabolites (ammonia, lactate, total volatile fatty acids) was highest in the Agriculture-Beech-Forest habitat (ABF). Correlations can be identified between adaptations in the microbiota and specific nutrient concentrations, as well as in strong fluctuations in ingested forage. In addition, a core bacterial community comprising five genera could be identified across all habitats, up to 44% of total relative abundance. As with all wild ruminants, many microbial genera remain largely unclassified at various taxonomic levels. This study provides a more in-depth insight into the diversity and complexity of the roe deer rumen microbiota. It highlights the key microorganisms responsible for converting naturally available nutrients of different botanical origins.

Bacterial communities and prevalence of antibiotic resistance genes carried within house flies (Diptera: Muscidae) associated with beef and dairy cattle farms.

House flies (Musca domestica Linnaeus) are vectors of human and animal pathogens at livestock operations. Microbial communities in flies are acquired from, and correlate with, their local environment. However, variation among microbial communities carried by flies from farms in different geographical areas is not well understood. We characterized bacterial communities of female house flies collected from beef and dairy farms in Oklahoma, Kansas, and Nebraska using 16S rDNA amplicon sequencing and PCR. Bacterial community composition in house flies was affected by farm type and location. While the shared number of taxa between flies from beef or dairy farms was low, those taxa accounted >97% of the total bacterial community abundance. Bacterial species richness was 4% greater in flies collected from beef than in those collected from dairy farms and varied by farm type within states. Several potential pathogenic taxa were highly prevalent, comprising a core bacterial community in house flies from cattle farms. Prevalence of the pathogens Moraxella bovis and Moraxella bovoculi was greater in flies from beef farms relative to those collected on dairy cattle farms. House flies also carried bacteria with multiple tetracycline and florfenicol resistance genes. This study suggests that the house flies are significant reservoirs and disseminators of microbial threats to human and cattle health.

Tree species mixing begets admixture of soil microbial communities: Variations along bulk soil, rhizosphere soil and root tissue

Tree species can substantially impact the structure and functioning of soil microbial communities. However, how tree species mixing affects soil microbial communities along different soil compartment niches remains unknown, despite the theoretical (e.g., plant-soil feedback) and practical (e.g., rhizosphere engineering) importance of such knowledge in understanding and managing forest ecosystems. In this study, we analyzed soil samples taken from three microhabitats (bulk soil, rhizosphere soil, and root tissue) of pure conifer species (Pinus massoniana) plantations (PP), pure broadleaf species (Castanopsis hystrix) plantations (PC), and mixed plantation forest of the two species (MF) to understand the effects of tree species mixing on core soil microbial communities. We found that the diversity of soil bacterial and fungal communities was not affected by tree species mixing in most cases, but community composition (relative abundance and functional composition) was largely shaped by tree species mixing. Non-metric multidimensional scaling (NMDS) analysis revealed that the core bacterial and fungal communities of MF were between those of PP and PC. This suggests that tree species mixing can lead to a combination of soil microbial communities associated with each of the two tree species, potentially resulting in higher nutrient contents in the bulk soil of MF and lower phosphorus and carbon limitations in both the bulk and rhizosphere soils of MF compared to those of PP and PC. The Mantel test and redundancy analysis (RDA) showed that pH and NO3–-N content were the main environmental variables influencing soil microbial communities. Overall, the effects of tree species mixing varied markedly with microhabitat and season, with rhizosphere soil having the highest microbial diversity and network complexity and root tissue having the lowest. These results suggest that the mixing effects of tree species are more pronounced in the rhizosphere and dry season, on which silvicultural practices should focus.

Unraveling the core bacterial community responsible for quality and flavor improvement of the radish paocai during spontaneous fermentation

The effects of different varieties of radish on the quality and flavor of radish paocai are still elusive. Herein, this study aimed to compare the quality and flavor of radish paocai fermented by three kinds of radish, and further investigate the core bacterial community that mainly positively correlated with the quality and flavor improvement of paocai. As fermentation proceeded, pH and nitrite decreased, total acid and reducing sugar increased, and salinity showed a fluctuating decrease. Besides, LL had the highest content of reducing sugar and free amino acids, and CB had more organic acids and umami amino acids than other kinds of paocai. The bacterial community analysis confirmed that the variety of radish had little impact on bacterial succession, and Weissella, Lactobacillus, and Leuconostoc were found to be the core bacterial community that could promote the increase of organic acids, free amino acids, and volatile flavor compounds. In particular, Weissella was the biomarker on day 4 of fermentation, and Lactobacillus was the biomarker on day 7 in three kinds of radish paocai. Collectively, using different varieties of radish did not significantly induce change in the bacterial community of the radish paocai, although these radish paocai products presented different qualities and flavors.

Metagenetic Analysis of the Pregnant Microbiome in Horses

Placentitis is the leading cause of infectious abortion in the horse. Additionally, it can result in weak and/or growth restricted offspring. While the etiology of ascending placentitis is well described in mares, less is known regarding the pathogenesis of other types, such as nocardioform placentitis. This study aims to identify the microbial communities in different body sites of the pregnant mare in early gestation to establish a core microbiome that may be perturbed in pathologic pregnancies such as placentitis. We hypothesize that the equine placenta harbors a distinct resident microbiome in early pregnancy when characterized by metagenetics and that there will be a disparity in bacterial communities from the oral, vaginal, and fecal microbiome. Samples were collected from the oral cavity, vagina, anus, and the allantoic portion of the allantochorion (“placenta”) from five pregnant mares between 96 and 120 days of gestation. The V4 region of the 16S rRNA gene was amplified for Illumina MiSeq sequencing to examine core bacterial communities present in the different body sites. Microbial community composition of the pregnant ponies by body site was significantly different (Bray–Curtis dissimilarity). The placenta was significantly different from the feces, oral cavity, and vagina. Alpha diversity measuring the Shannon diversity matrix was significant, with the body sites being a compounding variable, meaning there was a difference in richness and evenness in the different microbial communities. Feces had the greatest alpha diversity, while the oral cavity and placenta similarly had the least. In conclusion, metagenetics did reveal distinct community differences in the oral, fecal, vaginal, and placenta cavities of the horse. The equine placenta does show similarities in its microbial communities to the oral cavity. Further research needs to be completed to investigate how bacteria may be translocated to the placenta from these other body sites and how they contribute to the development of placentitis.

Diversity and Dynamics of Bacterial Communities in the Digestive and Excretory Systems across the Life Cycle of Leafhopper, Recilia dorsalis.

Recilia dorsalis is a notorious rice pest that harbors numerous symbiotic microorganisms. However, the structure and dynamics of bacterial communities in various tissues of R. dorsalis throughout its life cycle remain unclear. In this study, we used high-throughput sequencing technology to analyze the bacterial communities in the digestive, excretory, and reproductive systems of R. dorsalis at different developmental stages. The results showed that the initial microbiota in R. dorsalis mostly originated from vertical transmission via the ovaries. After the second-instar nymphs, the diversity of bacterial communities in the salivary gland and Malpighian tubules gradually decreased, while the midgut remained stable. Principal coordinate analysis revealed that the structure of bacterial communities in R. dorsalis was primarily influenced by the developmental stage, with minimal variation in bacterial species among different tissues but significant variation in bacterial abundance. Tistrella was the most abundant bacterial genus in most developmental stages, followed by Pantoea. The core bacterial community in R. dorsalis continuously enriched throughout development and contributed primarily to food digestion and nutrient supply. Overall, our study enriches our knowledge of the bacterial community associated with R. dorsalis and provides clues for developing potential biological control technologies against this rice pest.