Dominant Bacterial Taxa Research Articles

Differences in bacterial diversity, composition, and community networks in lake water across three distinct regions on the Qinghai-Tibet Plateau

We analyze bacterial composition, diversity, geographical distribution, and their community networks in lake water in three adjacent regions on the Qinghai-Tibet Plateau (QTP). Results show that bacterial alpha-diversity indices are much lower in the Hoh Xil (HX) than that in the Yellow River Headwater (YRH) regions and the Qaidam (QD) region. The dominant phyla in QD and YRH are Proteobacteria which account for 42.45 % and 43.64 % of all detected phyla, while Bacteroidetes is the dominant bacterial taxa in HX (46.07 %). Redundancy analysis results suggest that the most important factors in driving bacterial community composition in the three regions are altitude (QD), total nitrogen (YRH), and pH (HX), respectively. Both environmental factors and spatial factors significantly affect the bacterial community composition in QD and HX, while only environmental factors are the major drivers in YRH. Finally, network analyses reveal that the bacterial network structure in QD is more complex than those in YRH and HX, whereas the bacterial network in HX is the most stable, followed by those in QD and YRH.

Different facets of bacterial and fungal communities drive soil multifunctionality in grasslands spanning a 3500 km transect

Abstract Soil microbial communities are essential in regulating ecosystem functions and services. However, the importance of bacterial and fungal communities as predictors of multiple soil functions (i.e. soil multifunctionality) in grassland ecosystems has not been studied systematically. Here, we measured soil microbial diversity, community composition, biomass and multiple soil functions of 41 sites in five grassland ecosystems spanning a 3500 km northeast–southwest transect. The random forest algorithm was adopted to determine the importance of geographical location, climatic, altitude, edaphic, plant and microbial predictors in driving a proxy of soil multifunctionality (seven soil functions in this study). Moreover, structural equation models were employed to examine the direct and indirect effects of those predictors on soil multifunctionality. Our results demonstrated that soil multifunctionality was positively driven by soil fungal diversity but not by bacterial diversity. Fungal phylogenetic diversity (presence of different evolutionary lineages) showed stronger positive relationships with soil multifunctionality than taxonomic diversity (richness of species). Dominant bacterial taxa, particularly of phyla Actinobacteria and Proteobacteria, were positively associated with soil multifunctionality, while none of the fungal taxa were found to regulate soil multifunctionality. Furthermore, both fungal and bacterial biomass had significant effects on soil multifunctionality, while the effect of microbial biomass was weaker than that of fungal diversity and bacterial taxa. Importantly, the direct positive effects of soil fungal diversity, dominant bacterial taxa, and fungal and bacterial biomass were maintained after accounting for multiple predictors in grassland ecosystems. This study provided strong empirical evidence that soil multifunctionality was driven by different facets of the bacterial and fungal communities in the grassland ecosystems. Our results also highlighted that any loss of fungal diversity, dominant bacterial taxa and microbial biomass might reduce soil multifunctionality, exacerbating ecosystem functions and services such as soil fertility, primary production and climate mitigation in grassland ecosystems. Read the free Plain Language Summary for this article on the Journal blog.

Microbiota and Serum Metabolic Profile Changes in Korean Native Hanwoo Steer in Response to Diet Feeding Systems.

The diversity of bacteria and their function in cattle gastrointestinal tracts can influence animal welfare. Next-generation sequencing (NGS) was used to investigate microbial diversity in the feces of Hanwoo steers reared under natural grazing (GS) and housing (HS) systems. Additionally, serum metabolic parameters, such as liver and kidney markers and mineral and lipid content changes, as well as their correlation with pyrotags, were studied. A total of 6468 ± 87.86 operational taxonomic units (OTUs) were identified in both steer groups, of which 3538 ± 38.17 OTUs were from grazing steer and 2930 ± 94.06 OTUs were from GS. Chao1 index analysis revealed a higher bacterial richness in GS. The dominant bacterial taxa were Bacteroidetes and Firmicutes. GS showed lower Bacteroidetes and higher Firmicutes abundance than HS. The serum of HS showed consistent increases in gamma-glutamyl transpeptidase (γGTP), glucose (GLU), total cholesterol (T-CHO), and triglyceride (TG) levels. The impact of GS on animal health and serum metabolic markers was strongly correlated with microbiota. As shown in this study, grazing has a significant impact on the fecal microbiota at the phylum and family levels, as well as the serum biochemical metabolites of Hanwoo steers.

Soil Bacterial Community Structure in Different Micro-Habitats on the Tidal Creek Section in the Yellow River Estuary

Tidal creeks have attracted considerable attention in estuary wetland conservation and restoration with diverse micro-habitats and high hydrological connectivity. Bacterial communities act effectively as invisible engines to regulate nutrient element biogeochemical processes. However, few studies have unveiled the bacterial community structures and diversities of micro-habitats soils on the tidal creek section. Our study selected three sections cross a tidal creek with obviously belt-like habitats “pluff mudflat – bare mudflat – Tamarix chinensis community – T. chinensis-Suaeda salsa community– S. salsa community” in the Yellow River estuarine wetland. Based on soil samples, we dissected and untangled the bacterial community structures and special bacterial taxa of different habitats on the tidal creek section. The results showed that bacterial community structures and dominant bacterial taxa were significantly different in the five habitats. The bacterial community diversities significantly decreased with distance away from tidal creeks, as well as the dominant bacteria Flavobacteriia and δ-Proteobacteria, but in reverse to Bacteroidetes and Gemmatimonadetes. Moreover, the important biomarkers sulfate-reducing bacteria and photosynthetic bacteria were different distributions within the five habitats, which were closely associated with the sulfur and carbon cycles. We found that the bacterial communities were heterogeneous in different micro-habitats on the tidal creek section, which was related to soil salinity, moisture, and nutrients as well as tidal action. The study would provide fundamental insights into understanding the ecological functions of bacterial diversities and biogeochemical processes influenced by tidal creeks.

A high-throughput DNA sequencing study of fecal bacteria of seven Mexican horse breeds.

Horses are non-ruminant, herbivorous mammals, been used through history for various purposes, with a gut microbiota from cecum to the colon, possessing remarkable fermentative capacity. We studied the fecal microbiota of Azteca, Criollo, Frisian, Iberian, Pinto, Quarter and Spanish horse breeds living in Mexico by next-generation DNA sequencing of 16S rRNA gene libraries. Dominant phyla Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes, Fibrobacteres, Actinobacteria and Verrucomicrobia have different relative abundances among breeds, with contrasted alpha and beta diversities as well. Heatmap analysis revealed that Ruminococcaceae, Lachnospiraceae, Mogibacteriaceae families, and order Clostridiales are more abundant in Spanish, Azteca, Quarter and Criollo breeds. The LEfSe analysis displayed higher abundance of order Bacteroidales, family BS11, and genera Faecalibacterium, Comamonas, Collinsella, Acetobacter, and Treponema in Criollo, Azteca, Iberian, Spanish, Frisian, Pinto, and Quarter horse breeds. The conclusion is that dominant bacterial taxa, found in fecal samples of horse breeds living in Mexico, have different relative abundances.

The Effects of a Typhoon on the Dynamic of Microbial Community Structure and Water Quality of the Marine Bathing Beach

Dalian Jinshitan beach was chosen to evaluate the impact of a typhoon on the bacterial community structure and water quality of a marine bathing beach. The concentration of enterococci was determined by the cultivation method. The bacterial community structure and abundance were analyzed using the 16S rDNA next-generation sequencing and qPCR methods. Results showed that the abundance of cultivable enterococci both in alongshore and offshore seawater increased, while it decreased in dry, wet and submerged sand. The water quality deteriorated immediately after the typhoon, and nearly recovered one month after the typhoon. The typhoon event also decreased the bacterial abundance and changed the bacterial community of the beach. Sphingomonadaceae and Rhodobacteraceae significantly increased in seawater and decreased in dry sand immediately after the typhoon. Human and other fecal taxa increased in water and sand. One month after the typhoon, the diversity and many dominant bacterial taxa nearly recovered in seawater and wet sand. Our work shows that the typhoon changed the bacterial dynamics, deteriorated the water quality and proved the transportation of bacterial taxa and input of fecal pollution between water and beach sand or land. Apart from the impact of the typhoon, the geographical location was another important factor in the changed bacterial community.

Three-dimensional imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa

Improving our understanding of host–microbe relationships in the gut requires the ability to both visualize and quantify the spatial organization of microbial communities in their native orientation with the host tissue. We developed a systematic procedure to quantify the three-dimensional (3D) spatial structure of the native mucosal microbiota in any part of the intestines with taxonomic and high spatial resolution. We performed a 3D biogeographical analysis of the microbiota of mouse cecal crypts at different stages of antibiotic exposure. By tracking eubacteria and four dominant bacterial taxa, we found that the colonization of crypts by native bacteria is a dynamic and spatially organized process. Ciprofloxacin treatment drastically reduced bacterial loads and eliminated Muribaculaceae (or all Bacteroidetes entirely) even 10 d after recovery when overall bacterial loads returned to preantibiotic levels. Our 3D quantitative imaging approach revealed that the bacterial colonization of crypts is organized in a spatial pattern that consists of clusters of adjacent colonized crypts that are surrounded by unoccupied crypts, and that this spatial pattern is resistant to the elimination of Muribaculaceae or of all Bacteroidetes by ciprofloxacin. Our approach also revealed that the composition of cecal crypt communities is diverse and that Lactobacilli were found closer to the lumen than Bacteroidetes, Ruminococcaceae, and Lachnospiraceae, regardless of antibiotic exposure. Finally, we found that crypts communities with similar taxonomic composition were physically closer to each other than communities that were taxonomically different.

Differential Effects of Natural Grazing and Feedlot Feeding on Yak Fecal Microbiota.

Variation in food and diet shapes the diversity of the gut microbiota of ruminants. The present study investigated the microbial diversity in the fecal microbiota of yaks reared under natural grazing and feedlot system. A total of 48 domestic yaks with an average age of 7.5 years were selected from two different grazing habitats: one group grazed on natural pasture (grazing yaks—GY) while the other group was fed fodder and concentrate (feedlot yaks—FY). Crude protein, non-fiber carbohydrate, hemicelluloses, and digestible dry matter contents of natural pastures were higher than those in the feedlot. The lower insoluble fiber contents were found in grazing land. The 16S rRNA gene sequencing revealed 675 and 348 unique operational taxonomic units (OTUs) in the GY and FY, respectively, in addition to 1,778 common OTUs. Overall, a total of 9,891 OTUs were identified as a whole, of which 6,160 OTUs were from GY and 3,731 were from FY. Shannon index analysis revealed a higher bacterial diversity in GY than FY. At the phylum level, Firmicutes were dominant bacterial taxa in both groups. The relative abundance of Firmicutes in GY (56% ± 0.05) was higher than in FY (41% ± 0.08). At the family level, GY had a significantly higher abundance of Ruminococcaceae (p < 0.001) and Rikenellaceae (p < 0.001) than FY, but FY had a significantly higher abundance of Prevotellaceae than GY (p < 0.001). At the genus level, abundances of Faecalibacterium, Alloprevotella, and Succinivibrio were higher in FY than in GY. This study presents novel information on fecal bacterial composition and diversity in yaks reared under two different production systems.

Effects of Host Plant and Insect Generation on Shaping of the Gut Microbiota in the Rice Leaffolder, Cnaphalocrocis medinalis.

Gut microbes in insects may play an important role in the digestion, immunity and protection, detoxification of toxins, development, and reproduction. The rice leaffolder Cnaphalocrocis medinalis (Guenée) (Lepidoptera: Crambidae) is a notorious insect pest that can damage rice, maize, and other gramineous plants. To determine the effects of host plants and generations on the gut microbiota of C. medinalis, we deciphered the bacterial configuration of this insect pest fed rice or maize for three generations by Illumina MiSeq technology. A total of 16 bacterial phyla, 34 classes, 50 orders, 101 families, 158 genera, and 44 species were identified in C. medinalis fed rice or maize for three generations. Host plants, insect generation, and their interaction did not influence the alpha diversity indices of the gut microbiota of C. medinalis. The dominant bacterial taxa were Proteobacteria and Firmicutes at the phylum level and Enterococcus and unclassified Enterobacteriaceae at the genus level. A number of twenty genera coexisted in the guts of C. medinalis fed rice or maize for three generations, and their relative abundances occupied more than 90% of the gut microbiota of C. medinalis. A number of two genera were stably found in the gut of rice-feeding C. medinalis but unstably found in the gut microbiota of maize-feeding C. medinalis, and seven genera were stably found in the gut of maize-feeding C. medinalis but unstably found in the gut of rice-feeding C. medinalis. In addition, many kinds of microbes were found in some but not all samples of the gut of C. medinalis fed on a particular host plant. PerMANOVA indicated that the gut bacteria of C. medinalis could be significantly affected by the host plant and host plant × generation. We identified 47 taxa as the biomarkers for the gut microbiota of C. medinalis fed different host plants by LEfSe. Functional prediction suggested that the most dominant role of the gut microbiota in C. medinalis is metabolism, followed by environmental information processing, cellular processes, and genetic information processing. Our findings will enrich the understanding of gut bacteria in C. medinalis and reveal the differences in gut microbiota in C. medinalis fed on different host plants for three generations.

Soil pH: a key edaphic factor regulating distribution and functions of bacterial community along vertical soil profiles in red soil of pomelo orchard

BackgroundSoil microbes exist throughout the soil profile and those inhabiting topsoil (0–20 cm) are believed to play a key role in nutrients cycling. However, the majority of the soil microbiology studies have exclusively focused on the distribution of soil microbial communities in the topsoil, and it remains poorly understood through the subsurface soil profile (i.e., 20–40 and 40–60 cm). Here, we examined how the bacterial community composition and functional diversity changes under intensive fertilization across vertical soil profiles [(0–20 cm (RS1), 20–40 cm (RS2), and 40–60 cm (RS3)] in the red soil of pomelo orchard, Pinghe County, Fujian, China.ResultsBacterial community composition was determined by 16S rRNA gene sequencing and interlinked with edaphic factors, including soil pH, available phosphorous (AP), available nitrogen (AN), and available potassium (AK) to investigate the key edaphic factors that shape the soil bacterial community along with different soil profiles. The most dominant bacterial taxa were Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Crenarchaeota, and Bacteriodetes. Bacterial richness and diversity was highest in RS1 and declined with increasing soil depth. The distinct distribution patterns of the bacterial community were found across the different soil profiles. Besides, soil pH exhibited a strong influence (pH ˃AP ˃AN) on the bacterial communities under all soil depths. The relative abundance of Proteobacteria, Actinobacteria, Crenarchaeota, and Firmicutes was negatively correlated with soil pH, while Acidobacteria, Chloroflexi, Bacteriodetes, Planctomycetes, and Gemmatimonadetes were positively correlated with soil pH. Co-occurrence network analysis revealed that network topological features were weakened with increasing soil depth, indicating a more stable bacterial community in the RS1. Bacterial functions were estimated using FAPROTAX and the relative abundance of functional bacterial community related to metabolic processes, including C-cycle, N-cycle, and energy production was significantly higher in RS1 compared to RS2 and RS3, and soil pH had a significant effect on these functional microbes.ConclusionsThis study provided the valuable findings regarding the structure and functions of bacterial communities in red soil of pomelo orchards, and highlighted the importance of soil depth and pH in shaping the soil bacterial population, their spatial distribution and ecological functioning. These results suggest the alleviation of soil acidification by adopting integrated management practices to preserve the soil microbial communities for better ecological functioning.

Vertical distribution patterns and drivers of soil bacterial communities across the continuous permafrost region of northeastern China

BackgroundSoil microorganisms in the thawing permafrost play key roles in the maintenance of ecosystem function and regulation of biogeochemical cycles. However, our knowledge of patterns and drivers of permafrost microbial communities is limited in northeastern China. Therefore, we investigated the community structure of soil bacteria in the active, transition and permafrost layers based on 90 soil samples collected from 10 sites across the continuous permafrost region using high-throughput Illumina sequencing.ResultsProteobacteria (31.59%), Acidobacteria (18.63%), Bacteroidetes (9.74%), Chloroflexi (7.01%) and Actinobacteria (6.92%) were the predominant phyla of the bacterial community in all soil layers; however, the relative abundances of the dominant bacterial taxa varied with soil depth. The bacterial community alpha-diversity based on the Shannon index and the phylogenetic diversity index both decreased significantly with depth across the transition from active layer to permafrost layer. Nonmetric multidimensional scaling analysis and permutation multivariate analysis of variance revealed that microbial community structures were significantly different among layers. Redundancy analysis and Spearman’s correlation analysis showed that soil properties differed between layers such as soil nutrient content, temperature and moisture mainly drove the differentiation of bacterial communities.ConclusionsOur results revealed significant differences in bacterial composition and diversity among soil layers. Our findings suggest that the heterogeneous environmental conditions between the three soil horizons had strong influences on microbial niche differentiation and further explained the variability of soil bacterial community structures. This effort to profile the vertical distribution of bacterial communities may enable better evaluations of changes in microbial dynamics in response to permafrost thaw, which would be beneficial to ecological conservation of permafrost ecosystems.

Ecological aspects of postmortem microbiome and possibility of their use in forensic practice

Through experimental reproduction of the decomposition process using the cadaver of rabbit Oryctolagus sp., the dynamics of cadaver microflora was studied; the dominant bacterial taxa were isolated in pure culture and identified; their ecological and trophic profiles and biodiversity were described based on the values of Simpson and Menchinic ecological indices. The dependence of cadaver rotting and skeletonization rate on the taxonomic profile of microorganisms, decomposition period, and abiotic environmental factors (temperature, acidity, soil moisture) was demonstrated. The data obtained contribute to justifying the use of microbiological methods in forensic practice. To establish objective causality patterns of microbial transformation of organic matter in nature, further targeted study of ecological patterns of cadaveric microflora is necessary.

Spatial distribution of bacterioplankton community composition and their diversity in Lake Fuxian during thermal stratification period

水体垂向分层是深水湖泊一个重要的特征，这不仅影响水体理化环境因子，而且影响水生生物组成的垂向分布，但是对不同水层水体细菌的多样性和群落结构组成的形成与维持机制知之甚少. 本研究以抚仙湖为研究对象，在水体热力分层期间采集不同位点、不同水层水样，借助16S rDNA Illumina Miseq高通量测序技术，探究水体细菌多样性和群落结构组成的空间分布特征及关键影响因子. 研究结果表明：(1)抚仙湖北部湖心在水深15~40 m处出现温跃层，温度由23℃降至15℃，其余理化环境因子也存在明显的垂向分层现象；与垂向差异相比，表层水体各理化因子在水平方向上的差异相对较小. (2)在水平方向上，南部湖心表层水体细菌alpha多样性(Operational Taxonomic Unit数目和Faith's phylogenetic diversity)最高；在垂向上，水体细菌alpha多样性随着采样水深的增加呈现单峰分布，在30和40 m水层最高；水体细菌alpha和beta多样性的垂向差异均显著大于水平方向差异. (3)表层水体细菌主要由Actinomycetales、unidentified Cyanobacteria、Burkholderiales和Sphingobacteriales组成；温跃层中以Pseudomonadales为主；均温层的优势菌群为unidentified Chloroflexi、Actinomycetales和Burkholderiales. 典范对应分析表明溶解性有机碳、溶解氧、硝态氮、氨氮和总磷浓度是影响细菌群落组成的主要环境因子.;Deep lakes are typically characterized by thermal stratification throughout the year, except for a short mixing period in winter. This vertical partitioning has important effects on many biotic, physical and chemical characteristics of the water column. However, at present, little is known about how these changes affect the vertical distribution of bacterioplankton community diversity. In this study, Lake Fuxian with a relatively long thermal stratification period every year, was chosen for the investigation of bacterioplankton distribution, diversity and composition on August 25th, 2013. 16S rDNA Illumina Miseq high-throughput sequencing technology was performed on DNA extracted from water samples collected from different locations and different water depths. The results showed that: (1) A thermocline appeared in the lake center and in the northern part of this lake at the depth of 15-40 m, with the temperature dropping from 23℃ to 15℃. Other physical and chemical factors also showed obvious vertical stratification pattern. Horizontally, there is no significant difference in physicochemical features. (2) In the horizontal direction, the alpha diversities of plankton bacteria (the number of Operational Taxonomic Units and Faith's phylogenetic diversity) in the surface water of the southern lake center was the highest; in the vertical direction, the alpha diversity gradually increased with the increase of the sampling depth, topping at the depths of 30 m or 40 m, and then gradually decreased; the difference of the bacterioplankton alpha and beta diversity in the vertical direction was significantly greater than those in the horizontal direction. (3) The bacterioplankton in the epilimnion were mainly composed of Actinomycetales, unidentified Cyanobacteria, Burkholderiales and Sphingobacteriales; the relative abundance of Pseudomonadales in the thermocline significantly increased and became dominant; unidentified Chloroflexi, Actinomycetales and Burkholderiales were the dominant bacterial taxa in the hypolimnion. The canonical correspondence analysis demonstrated that the concentrations of dissolved organic carbon, dissolved oxygen, nitrate, ammonium and total phosphorus are the significant environmental variables shaping the bacterial community's composition and diversity.

Changes in precipitation regime lead to acceleration of the N cycle and dramatic N2O emission

Alpine meadows on the Qinghai-Tibetan Plateau are sensitive to climate change. The precipitation regime in this region has undergone major changes, “repackaging” precipitation from more frequent, smaller events to less frequent, larger events. Nitrous oxide (N2O) is an important indicator of responses to global change in alpine meadow ecosystems. However, little information is available describing the mechanisms driving the response of N2O emissions to changes in the precipitation regime. In this study, a manipulative field experiment was conducted to investigate N2O flux, soil properties, enzyme activity, and gene abundance in response to severe and moderate changes in precipitation regime over two years. Severe changes in precipitation regime led to a 12.6-fold increase in N2O fluxes (0.0068 ± 0.0018 mg m−2 h−1) from Zoige alpine meadows relative to natural conditions (0.0005 ± 0.0029 mg m−2 h−1). In addition, severe changes in precipitation regime significantly suppressed the activities of leucine amino peptidase (LAP) and peroxidase (PEO), affected ecoenzymatic stoichiometry, and increased the abundances of gdhA, narI and nirK genes, which significantly promoted organic nitrogen (N) decomposition, denitrification, and anammox processes. The increase in abundance of these genes could be ascribed to changes in the abundance of several dominant bacterial taxa (i.e., Actinobacteria and Proteobacteria) as a result of the altered precipitation regime. Decreases in nitrate and soil moisture caused by severe changes in precipitation may exacerbate N limitation and water deficit, lead to a suppression of soil enzyme activity, and change the structure of microorganism community. The N cycle of the alpine meadow ecosystem may accelerate by increasing the abundance of key N functional genes. This would, in turn, lead to increased N2O emission. This study provided insights into how precipitation regimes changes affect N cycling, and may also improve prediction of N2O fluxes in response to changes in precipitation regime.

Study of Heavy Metals and Microbial Communities in Contaminated Sediments Along an Urban Estuary

Estuarine sediments are increasingly contaminated by heavy metals as a result of urbanization and human activities. Continuous multi-heavy metal accumulation in the ecosystem can provoke new effects on top of the complex environmental interactions already present in estuarine ecosystems. It is important to study their integrated influence on imperative microbial communities to reflect on the environmental and ecological risks they may impose. Inductively coupled plasma optical emission spectroscopy analysis for five metals Cd, Cr, Cu, Pb, and Zn showed that Cr and Cu concentrations in intertidal sediments of the urbanized Yangtze River estuary in China have consistently exceeded respective threshold effect concentration (TEC) levels. The geo-accumulation and potential ecological risk index results of the five metals showed that all sampling sites were weakly to moderately polluted, and at considerable to high ecological risk, respectively. Redundancy and correlation analyses showed that Zn followed by Cr in the ecosystem were explanatory of the shifts in recorded microbial community structures. However, the spatial variation in metal concentrations did not correspond to the selection of metal resistance genes (MRGs). Unlike many other dominant bacterial taxa, most of the sulfate-reducing bacteria (SRB) and associated sulfate respiration as the dominant microbially contributed ecological function were found to negatively correlate with Zn and total heavy metal pollution. Zn concentration was proposed to be a potent indicator for heavy metal pollution-associated microbial community compositional shifts under urbanized estuarine conditions. The associations between heavy metals and estuarine microbial communities in this study demonstrate the influence of heavy metals on microbial community structure and adaptations that is often overshadowed by environmental factors (i.e., salinity and nutrients).

The appropriate dose of Bacillus cereus improves the homeostasis of intestinal microbiota but does not significantly influence microbial functions in Paramisgurnus dabryanus

The intestinal microbiota play a vital role in the growth and health of the host. Probiotics could influence the homeostasis of intestinal microbiota, but the relationship between species and ecosystem stability is poorly understood. Here, four diets with different doses of Bacillus cereus (control, 0 cfu/kg; BL7, 107 cfu/kg; BL9, 109 cfu/kg; and BL11, 1011 cfu/kg) were designed to investigate the intestinal microbiota in Paramisgurnus dabryanus. The growth experiment demonstrated that the growth performance and the indices of Chao1, phylogenetic diversity, Simpson and Shannon improved significantly after loaches were fed a BL11 diet. The dominant composition of intestinal microbiota at phylum, class and genus levels did not change in loach after feeding different diets. Categories of bacterial taxa revealed that rare taxa and conditionally rare taxa were the dominant bacterial taxa in intestinal microbiota of loach. B. cereus supplemented with 1011 cfu/kg promoted the stability of the ecological network of intestinal microbiota by reinforcing the cooperation of interspecific interactions, promoting operational taxonomic units to shape larger submodules and increasing module hubs species and connectors species. Results of functional prediction revealed that a total of 5692 functions were shared among the four groups, which accounted for 91.7% of overall functions. To sum up, dietary supplementation with B. cereus had no significant influences on the composition and bacterial taxa of intestinal microbiota and the composition of bacterial functions. A dose of B. cereus appropriate to the diet could improve the growth performance and promote the homeostasis of intestinal microbiota in loach.

Reproductive tract microbiota of women in childbearing age shifts upon gynecological infections and menstrual cycle

BackgroundThis study was undertaken to discover whether the vaginal microbe of women at childbearing age is different among groups defined by urogenital tract infections, childbearing history and menstrual cycle, respectively.ResultsThis was a multiple case-control study of women at childbearing age who were assigned to case or control groups according to their states of urogenital tract infections. The participants were also grouped by childbearing history and menstrual cycle. Vaginal swabs were collected and stored at − 70 °C until assayed. The V3-V4 region of 16S rRNA gene was amplified using PCR and sequenced on the Illumina MiSeq platform. We tested the hypothesis of whether the relative abundance of microbial species in vaginal microbiota was varied with urogenital tract infections, childbearing history and menstrual cycle. The vaginal microbial richness (Alpha diversity measured by PD_whole tree) was decreased in normal women (without reproductive tract infections) than in those with bacterial vaginosis (BV), and decreased in pregnant women than in other groups of non-pregnancy. Similarly, women from groups of normal and in pregnancy had lower beta diversity on measure of unweighted_unifrac distance in comparison to those of infected and non-pregnant. The top 10 genus relative abundance, especially Lactobacillus, which was the most dominant genus with the relative abundance of 71.55% among all samples, did not differ significantly between groups of childbearing history and menstrual cycle analyzed by ANOVA and nonparametric kruskal_wallis. Lactobacillus iners and Lactobacillus helveticus have the most abundance, totally account for 97.92% relative abundance of genus Lactobacillus. We also found that a higher L.helveticus/L.iners ratio is more likely to present in normal women than in the infected and in pregnant than in non-pregnant, although these comparisons lack statistical significance.ConclusionsThe relative abundance of dominant bacterial taxa in vaginal microbial communities of women at childbearing age were not different among groups of childbearing history and menstrual cycle. Women from groups of in pregnancy and without reproductive tract infections had lower alpha and beta diversity. The composition of the main lactobacillus species may shift upon phases of a menstrual cycle and the status of reproductive tract infections.

Vaginal microbiome Lactobacillus crispatus is heritable among European American women

The diversity and dominant bacterial taxa in the vagina are reported to be influenced by multiple intrinsic and extrinsic factors, including but not limited to pregnancy, contraceptive use, pathogenic states, socioeconomic status, and ancestry. However, the extent to which host genetic factors influence variation in the vaginal microbiota is unclear. We used a biometrical genetic approach to determine whether host genetic factors contribute to inter-individual differences in taxa from a sample of 332 twins who self-identified as being of African (44 pairs) or European ancestry (122 pairs). Lactobacillus crispatus, a major determinant of vaginal health, was identified as heritable among European American women (narrow-sense heritability = 34.7%, P-value = 0.018). Heritability of L. crispatus is consistent with the reduced prevalence of adverse reproductive disorders, including bacterial vaginosis and preterm birth, among women of European ancestry.

Seasonal fluctuations in symbiotic bacteria and their role in environmental adaptation of the scleractinian coral Acropora pruinosa in high-latitude coral reef area of the South China Sea

Coral-associated bacterial communities are paramount for coral ecosystems and holobiont health. However, the role of symbiotic bacteria in the adaptation of high-latitude corals to seasonal fluctuations remains underexplored. Therefore, we used 16S rRNA-based high-throughput sequencing to analyze the symbiotic bacterial diversity, composition, and core bacterial community in high-latitude coral and explored the seasonal fluctuation characteristics of symbiotic bacterial communities. We found that bacterial richness and α-diversity changed significantly across different seasons. Additionally, the community structure recombined seasonally, with different dominant bacterial phyla and genera in different seasons. However, the symbiotic bacterial community structures of Acropora pruinosa in winter and spring were similar. Proteobacteria were the dominant bacteria in spring, autumn, and winter. In summer, the dominant bacterial taxa were Bacteroidota and Proteobacteria. Ralstonia was the dominant bacterial genus in spring and winter, whereas in autumn, BD1-7_clade was dominant. Linear discriminant analysis effect size identified 20 abundant genera between the different groups. Core microbiome analysis revealed that 12 core bacterial operational taxonomic units were associated with A. pruinosa in all seasons, seven of which varied with the seasons, changing between dominant and rare. Distance-based redundancy and variation partitioning analyses revealed that sea surface temperature was the major contributor of variation in the microbial community structure. We hypothesized that the high diversity and abundance of symbiotic bacteria and the increase in Prosthecochloris abundance in coral in summer can help A. pruinosa maintain its physiological functions, ameliorating the negative physiological effects of the decrease in Symbiodiniaceae density under high-temperature stress. Thus, the rapid reorganization of the symbiotic bacterial community structure and core microflora in different seasons may allow the corals to adapt to large seasonal environmental fluctuations. In conclusion, seasonal variation of bacteria plays an important role in coral adaptation to large environmental fluctuations.

Limited Bacterial Removal in Full-Scale Stormwater Biofilters as Evidenced by Community Sequencing Analysis.

In urban areas, untreated stormwater runoff can pollute downstream surface waters. To intercept and treat runoff, low-impact or "green infrastructure" approaches such as using biofilters are adopted. Yet, actual biofilter pollutant removal is poorly understood; removal is often studied in laboratory columns, with variable removal of viable and culturable microbial cell numbers including pathogens. Here, to assess bacterial pollutant removal in full-scale planted biofilters, stormwater was applied, unspiked or spiked with untreated sewage, in simulated storm events under transient flow conditions, during which biofilter influents versus effluents were compared. Based on microbial biomass, sequences of bacterial community genes encoding 16S rRNA, and gene copies of the human fecal marker HF183 and of the Enterococcus spp. marker Entero1A, removal of bacterial pollutants in biofilters was limited. Dominant bacterial taxa were similar for influent versus effluent aqueous samples within each inflow treatment of either spiked or unspiked stormwater. Bacterial pollutants in soil were gradually washed out, albeit incompletely, during simulated storm flushing events. In post-storm biofilter soil cores, retained influent bacteria were concentrated in the top layers (0-10 cm), indicating that the removal of bacterial pollutants was spatially limited to surface soils. To the extent that plant-associated processes are responsible for this spatial pattern, treatment performance might be enhanced by biofilter designs that maximize influent contact with the rhizosphere.