Number Of Operational Taxonomic Units Research Articles

Gut microbiota is associated with differential metabolic characteristics: A study on a defined cohort of Africans and Chinese.

ObjectiveThis study intended to determine the associations between gut microbiota and glucose response in healthy individuals and analyze the connection between the gut microbiome and glucose-metabolism-related parameters.MethodsFecal bacterial composition and anthropometric, body composition, body fat distribution, and biochemical measures were analyzed. A 75-g oral glucose tolerance test (OGTT) was given to each participant to investigate changes in glucagon-like peptide 1 (GLP-1), insulin, and glucose. The whole body fat and the regions of interest of local body composition were analyzed using dual-energy X-ray absorptiometry (DEXA), and gut microbiota composition was assessed through variable regions (V3–V4) of the bacterial 16s ribosomal RNA gene using high-throughput sequencing techniques. Spearman correlation analysis was used to evaluate the association between gut microbiota and clinical and metabolic changes.ResultsThe number of operational taxonomic units (OTUs) demonstrated a reduction in the diversity and composition of gut microbiota associated with enhanced adiposity, dyslipidemia, insulin resistance, and hyperglycemia. The alpha diversity revealed that microbiota diversity, richness, and composition were higher in the African group and lower in the Chinese group. Principal coordinates analysis (PCoA) plots of beta diversity showed significant variability in gut microbial community structure between the two groups (p = 0.0009). LEfSe analysis showed that phylum Bacteroidetes was significantly more abundant in the Chinese group, and this group also harbored members of the order Bacteroidales, family Bacteroidaceae, and genus Bacteroides. In contrast, the phylum Verrucomicrobia was significantly more prevalent in the African group (all p < 0.05). Concerning species, metastats analysis revealed 8 species in the Chinese group and 18 species in the African group that were significantly abundant. Spearman’s correlation analysis demonstrated that gut microbiota correlated with the factors that related to glucose metabolism.ConclusionOur data suggest that there is an interaction between gut microbiota, host physiology, and glucometabolic pathways, and this could contribute to adiposity and pathophysiology of hyperlipidemia, insulin resistance, and hyperglycemia. These findings provide an important basis for determining the relation between the gut microbiota and the pathogenesis of various metabolic disorders.

Effects of Broad-Spectrum Antibiotic (Florfenicol) on Resistance Genes and Bacterial Community Structure of Water and Sediments in an Aquatic Microcosm Model.

This study evaluates the effects of a broad-spectrum antibiotic (florfenicol) on antibiotic resistance genes (ARGs) and bacterial community structure in aquatic environments. We constructed an indoor aquatic microcosm model, adding different concentrations of florfenicol (0.1, 1, 10, 100 mg L−1), and water and sediment samples were collected after 0, 7, 30, and 60 days. qPCR and 16S rDNA amplicon sequencing were used to study the changes in the ARGs and bacterial community structure of the collected samples. The results show that the inclusion of florfenicol resulted in an increased abundance of the floR and optrA genes. Adding 100 mg L−1 florfenicol to the water increased the abundance of optrA gene copies with the maximum on the Day 7, and increased the abundance of floR gene copies with the maximum on Day 30. Adding 100 mg L−1 florfenicol to the sediment increased the abundance of floR and optrA genes by one order of magnitude on Day 60. Meanwhile, the average number of operational taxonomic units (OTUs) in the water samples was 257, and the average number of OTUs in sediment samples was 823. The bacterial community diversity and richness in sediments were higher than those in water. The difference between the maximal and minimal values of the Shannon diversity index in the water and sediment samples was 4.36 and 1.95, respectively. The effect of florfenicol on the bacterial community structure in water was much higher than that in sediment. At 30 days, the diversity index and richness index of the florfenicol treatment groups with 1 and 10 mg L−1 concentrations began to increase; at 60 days, the diversity and richness indices of the 100 mg L−1 florfenicol treatment group began to increase. The samples at the same sampling time in the sediments clustered closer together. The results of this study provide a scientific basis for guiding the rational use of florfenicol in aquaculture, maintaining a healthy and stable microecological environment in aquaculture, and provide theoretical data for environmental ecological risk assessment and safety management caused by microbial resistance under the abuse of florfenicol.

Effect of Lactobacillus reuteri S5 Intervention on Intestinal Microbiota Composition of Chickens Challenged with Salmonella enteritidis.

Simple SummaryThe interaction between intestinal microbiota and host plays a key role in the development of intestinal diseases. Salmonella enteritidis infection is a common cause of human gastroenteritis, which can lead to gastrointestinal dysfunction and microecological disorder. It is an important public health problem all over the world. Lactic acid bacteria are among the main probiotics in the intestinal microbiota, which is one of the main defense lines against intestinal pathogens. It is now also considered to be an effective alternative antibiotic to fight pathogenic bacterial infections. In order to explore the potential mechanism of lactic acid bacteria against S. enteritidis infection, this study started from the perspective of lactic acid bacteria regulating the intestinal microbiota and the infection of antigenic bacteria. The probiotic strain Lactobacillus reuteri S5 (L. reuteri S5) was used to establish an animal model of S. enteritidis infection in broilers. The regulatory effect of L. reuteri S5 on the intestinal microbiota structure of chickens infected with S. enteritidis is studied by high throughput sequencing technology. The results showed that L. reuteri S5 could regulate the composition and abundance of intestinal microbiota and resist the infection of S. enteritidis.To understand the mechanism of lactic acid bacteria against Salmonella enteritidis infection; we examined how lactic acid bacteria regulated the intestinal microbiota to resist infection by pathogenic bacteria. The probiotic strain Lactobacillus reuteri S5 was used to construct an animal model of S. enteritidis infected broilers. A high-throughput sequencing technology was used to analyze the regulatory effects of L. reuteri S5 on the structure of the intestinal microbiota of broilers infected with S. enteritidis; and to examine the possible defense mechanism they used. Our results showed that the administration of L. reuteri S5 reduced colonization of S. enteritidis (p < 0.05), decreased intestinal permeability (p < 0.05), and reduced the bacterial displacement likely due by S. enteritidis colonization (p < 0.05), suggesting some enhancement of the intestinal barrier function. Furthermore, L. reuteri S5 increased the number of operational taxonomic units (OTUs) in the chicken cecal microflora and the relative abundance of Lactobacillaceae and decreased the relative abundance of Enterobacteriaceae. These results suggest that the lactic acid bacterium L. reuteri S5 protected the intestinal microbiota of chickens against S. enteritidis infection.

Reducing Carbon Input Improved the Diversity of Bacterial Community in Large-Scale Biofloc Shrimp Culture Facilities

In this study, a group of large-scale biofloc shrimp culturing facilities were designed. The bioflocs were domesticated by continuously reducing the ratio of carbon to feed. The bacterial community diversity on the 20th, 40th, 60th, and 80th days was analyzed by high-throughput sequencing technology. The results showed that the biofloc content (0~16.8 ± 4.3) mL/L, TSS concentration (0~247.46 ± 27.3) mL/L, total ammonia nitrogen concentration (0~0.28 ± 0.052) mg/L, nitrite nitrogen concentration (0~4.13 ± 1.42) mg/L, nitrate nitrogen concentration (108.57 ± 19.6) mg/L were all within the safe concentration range of Litopenaeus vannamei. With the progress of reducing carbon input, the Chao1 index, the number of operational taxonomic units, and the Shannon index increased significantly. The number of OTUs of B80 (572.36 ± 13.26) was significantly higher than that of B60 (489.69 ± 12.97), B40 (423.35 ± 18.46) and B20 (407.67 ± 15.65) (p &lt; 0.05). The Chao1 index of B80 (768.58 ± 36.96) was significantly higher than that of B60 (646.8 ± 52.53), B40 (569.7 ± 46.53) and B20 (516.3 ± 21.35) (p &lt; 0.05). The Shannon index of B80 (5.63 ± 0.16) was higher than that of B60 (4.85 ± 0.13), B40 (4.68 ± 0.21) and B20 (3.65 ± 0.22), with significant difference (p &lt; 0.05). At the end of the experiment, the domestication formed a micro-ecosystem with Proteobacteria as the carrier (46.98 ± 15.82%), Chloroflexi as the skeleton (2.2 ± 0.36%), Nitrospirae (1.35 ± 0.26%) as the main water treatment functional bacteria, and other bacteria as auxiliary nitrogen and phosphorus removal; At the genus level, unclassified_f_Rhodobacteracea (22.97 ± 3.82%), Ruegeria (10.35 ± 1.26%), Muricauda (5.73 ± 0.61%), Algoriphagus (3.75% ± 0.85%) and Nitrospira (1.56 ± 0.56%) are the dominant bacteria. Under the synergistic effect of the above bacteria, the biofloc system remains relatively stable. The survival rate and unit yield of shrimp were (65.32 ± 6.85)% and (4.15 ± 1.58) kg/m3, respectively.

Comparison of tumor-associated and nontumor-associated esophageal mucosa microbiota in patients with esophageal squamous cell carcinoma.

Esophageal microbiota plays important roles in esophageal squamous cell carcinoma (ESCC). The aims of this study were to clarify the changes in the bacterial community during ESCC development and identify latent pathogenic bacteria which may contribute to esophageal carcinogenesis and progression. Fresh tumor and nontumor esophageal mucosal samples were collected from 31 men with ESCC. High-throughput 16s rRNA sequencing was performed, and the operational taxonomic unit data and bacterial classification annotation were obtained and analyzed. The Ace, Chao, Shannon, Simpson indexes, and operational taxonomic unit numbers were higher in nontumor tissues than in tumor tissues, although without statistical significance. There were 4 phyla and 28 genera found to show significant differences between tumor and nontumor samples. The general probiotic Lactobacillus was 1.98-fold higher in nontumor tissues, while the general pathogenic genera Fusobacterium was 4.35-fold higher in tumor tissues. For tumor tissue samples, the genera Treponema and Brevibacillus were significantly higher in N1 and N2 stages, respectively, and Acinetobacter was significantly higher in T3 stage. For nontumor tissues, the genus Fusicatenibacter was significantly higher in T2 stage, and Corynebacterium, Aggregatibacter, Saccharimonadaceae-TM7x, and Cupriavidus were significantly higher in T4 stage. Additionally, bacteria related to nitrotoluene degradation were enriched in nontumor tissues, while bacteria related to base excision repair were enriched in tumor tissues. The relative abundance of several phyla and genera are different between tumor and nontumor tissue samples. The altered bacterial microbiota is correlated with different tumor stages and some microbes may take part in the carcinogenesis and development of ESCC.

Exploring the diversity of leaf beetles (coleoptera: chrysomelidae) on the islands of Vietnam: a survey of Phu Quoc Island, South of Vietnam

Chrysomelidae on the islands of Vietnam has been poorly known. In this study, we investigated the diversity of Chrysomelidae on Phu Quoc Island in Kien Giang province, Southern Vietnam. Specimens were collected from Phu Quoc national park and the buffer zone forest. First, all specimens were ordered into a morph-species operational taxonomic unit (OTU). We collected 52 morphological OTUs of 31 genera and 5 subfamilies, 20 of which were identified as level species. Then, all morphological OTUs were extracted, amplified, and sequenced from the 658 bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. A total of 63 DNA barcode sequences of 13 species and 27 morphological OTUs were successfully sequenced and assigned to 32 Barcode Index Numbers (BIN) in Bold. In the comparison, between morphological OTUs and BINs, the number of OTUs was reduced to 20 species and 24 OTUs (a total of 44 OTUs). The number of species on Phu Quoc Island is estimated to be 1.38x –1. 96 × greater. A total of 32 BINs were generated from this study, 30 of which were new to Vietnam and 28 of which were new to BOLD. The results of this study provide the first document of the leaf beetle fauna on Phu Quoc island and the first DNA Barcoding data for Chrysomelidae from this region in Vietnam, as well as additional documents of leaf beetles on islands from another world.

The effect of sheep grazing abandonment on soil bacterial communities in productive mountain grasslands

Livestock grazing abandonment entails important shifts on the overall ecosystem function, but the effects of this land-use change on specific bacterial taxa remain poorly understood in mountain grasslands. Moreover, we currently lack knowledge about the feedbacks between changes in ecosystem functions affected by livestock abandonment in mountain grasslands and the soil bacterial communities. Here, we evaluated the behavior of bacterial communities' structure and composition at taxa level as a function of short (1-year) and long-term (15-years) grazing abandonment in a mountain grassland. We also linked the observed responses in the bacterial communities to changes in several ecosystem functions (i.e. primary production, plant species biodiversity, carbon stocks and soil fertility). The alpha diversity of the bacterial communities did not show a significant response as a consequence of grazing abandonment. However, we identified significant changes on the overall composition of soil bacterial communities between the long-term abandoned grassland areas and grazed or abandoned areas in the short term. We also evidenced a balance between the number of operational taxonomic units (OTUs) whose relative abundance is favored by livestock grazing (19.51 %) and those with higher relative abundances in long-term grazing exclusion areas (20.23 %) that could behave as indicators of grazing abandonment. Structural Equation Modeling analyses proved that several bacterial taxa associated with relevant ecosystem functions, such as Rhodospirillales order within Alphaproteobacteria phylum, featured significant changes in their relative abundance between grazing treatments. The direct and indirect effects of grazing exclusion on woody species encroachment and soil organic carbon were strongly linked to the changes in the abundance of bacterial taxa indicators. The assessment of the bacterial community response to livestock abandonment in mountain grasslands may thus provide early warning signs before subtle changes in ecosystem functions occur.

Characterization of the unique oral microbiome of children with Down syndrome

Down syndrome creates an abnormal oral environment, including susceptibility to periodontal disease at a young age, but there are no detailed studies of the oral microbiome in children with Down syndrome. In this study, we performed a comprehensive analysis of the oral bacteria of 40 children with Down syndrome and 40 non-Down syndrome children. Microbial DNA was extracted from dental plaque specimens and the V4 hypervariable region of the bacterial 16S rRNA gene was analyzed using the MiSeq platform. There were significant differences between the Down syndrome and non-Down syndrome groups in mean numbers of operational taxonomic units, and α- and β-diversity (P < 0.05). Interestingly, significant differences in α- and β-diversity between the two groups were only observed in subjects with gingival inflammation, but not in those without gingival inflammation (P < 0.05). Taxonomic analysis at the genus or species levels showed significant differences in relative abundance levels of certain bacteria between the Down syndrome and non-Down syndrome groups, including Corynebacterium, Abiotrophia and Lautropia (P < 0.05). These results suggest that children with Down syndrome may have a unique oral microbiome that could impact the development of dental diseases common in people with the syndrome.

Molecular diversity of foraminiferal eDNA in sediments and their correlations with environmental factors from the Yellow Sea

Foraminiferal environmental DNA (eDNA) is an efficient and reliable indicator of environmental changes. Here, we investigated the foraminiferal diversity of 25 stations (33–36°N) in the Yellow Sea based on eDNA and presented the first assessment on the correlations between foraminifera diversity and environmental conditions in the region. A total of 71 sediment samples were collected and local environmental parameters were measured. The foraminiferal eDNA was extracted from the samples and part of the small subunit (SSU) rRNA gene was amplified from the samples. After high–throughput sequencing, 1,701,899 amplified reads were detected and clustered into 426 operational taxonomic units (OTUs). The benthic foraminiferal eDNA community diversity and group diversity showed significant positive correlations with water depth and total inorganic carbon (TIC) in sediments, and significant negative correlations with temperature and total organic carbon (TOC) in sediments. However, in terms of the correlation between relative abundance and environmental factors, there were wide variations from species to species. In this work, planktic foraminiferal eDNA was detected in the sediments, and its OTUs number could reflect the changes in ocean currents and upper layer water masses to a certain extent. This is the first study on relationship of foraminiferal eDNA and environmental factors in the Yellow Sea shelf region of the western Pacific Ocean, and it demonstrates that community parameters in foraminiferal eDNA could be a valuable proxy for environmental changes in the shelf sea.

Metabolite profiling reveals insights into the species-dependent cold stress response of the green seaweed holobiont Ulva (Chlorophyta)

The green seaweed Ulva (Chlorophyta) and its associated epibacterial microbiome form a functional holobiont that adapts to stress as a whole. As the macroalga provides carbon sources for bacteria and relies on algal growth and morphogenesis-promoting factors (AGMPF) released by bacteria, those cross-kingdom interactions are especially fascinating. We hypothesized that the Ulva holobionts from the warm-temperate Mediterranean-Atlantic and cold Antarctic habitats respond to cold stress differently depending on the production of highly polar low molecular weight compounds (LMWCs) with stress-regulating activity. We compared the microbiome of and metabolic changes in U. compressa (cultivar U. mutabilis ), initially collected in Ria Formosa (Portugal), with that of U. bulbosa (strain AWI #1002) collected in Antarctica by performing a warm-cold temperature shift experiment. Microbiome analysis indicated significant differences between the two species and that the number of operational taxonomic units (OTUs) was lower in cultivated U. bulbosa than in freshly isolated Ulva ; despite this, AGMPF-producing bacteria were detected in both holobionts. Significant differences in metabolite profiles were observed between both species using hydrophilic interaction liquid chromatography coupled with electrospray ionization mass spectrometry (HILIC-ESI-MS). Biomarkers such as dimethylsulfoniopropionate (DMSP) and taurine were identified following a temperature shift from 18 °C to 5 °C in the warm-temperate U. mutabilis and the cold-adapted U. bulbosa , respectively. Our findings show that metabolic changes in the holobiont in response to cold are species-dependent. To evaluate the contribution of the metabolic changes of bacteria and algae to the stress response, the reductionistic model system of the tripartite community formed by U. mutabilis and its two essential bacteria, Roseovarius sp. strain MS2 and Maribacter sp. strain MS6, which release all essential AGMPFs, was investigated. We examined the production of polar LMWCs in the presence and absence of bacteria following a shift to cold temperatures. Among the metabolites studied, ectoine ((4 S )-2-methyl-3,4,5,6-tetrahydropyrimidine-4-carboxylic acid) was only detected in the presence of bacteria, highlighting the role of bacteria in releasing compounds that mitigate environmental stresses through cold stress adaptation factors (CSAF). Our findings suggest that microbiome engineering will allow us to improve macroalgae adaptability to stressful situations, which can be further applied to the sustainable management of (land-based) aquaculture systems. • Algal growth and morphogenesis promoting bacteria were found in cultures of Ulva independently of their origin and habitat. • Low molecular weight compounds (LMWC) of the holobiont were examined upon cold stress. • Cold stress triggers diverse potential cryoprotectants in warm- and cold-adapted Ulva. • Taurine and DMSP may be considered as species-specific stress biomarkers. • Axenic Ulva cultures elucidate the bacterial contribution to the production of LMWC.

Campylobacter Species of the Oral Microbiota as Prognostic Factor for Cardiovascular Outcome after Coronary Artery Bypass Grafting Surgery.

Background: The oral microbiota has been implicated in a variety of systemic diseases, including cardiovascular (CV) disease. The main objective of this study (DRKS-ID: DRKS00015776) was to evaluate the prognostic importance of the oral microbiota for further CV events in patients undergoing coronary artery bypass grafting surgery (3-year follow-up). Methods: In this longitudinal cohort study, 102 CV patients were enrolled, of whom 95 completed the 3-year follow-up. The CV outcome was assessed using the major adverse cardiac and cerebrovascular events criteria. To evaluate subgingival colonization, 16S rRNA genes were amplified, targeting the V3/V4 region (Illumina MiSeq). Results: Regarding the specific number of operational taxonomic units (OTUs), no significant differences in CV outcome were determined (alpha diversity, Shannon index). In linear discriminant analyses and t-tests, the disease-specific differences in the beta diversity of the microbiota composition were evaluated. It was evident that bacteria species of the genus Campylobacter were significantly more prevalent in patients with a secondary CV event (p = 0.015). This hierarchical order also includes Campylobacter rectus, which is considered to be of comprehensive importance in both periodontal and CV diseases. Conclusions: Here, we proved that subgingival occurrence of Campylobacter species has prognostic relevance for cardiovascular outcomes in CV patients undergoing coronary artery bypass grafting.

Effect of fresh and spray-dried microalgal diets on the growth, digestive enzymatic activity, and gut microbiota of juvenile winged pearl oyster Pteria penguin

The effects of fresh and spray-dried microalgal diets on the growth, digestive enzymatic activity, and gut microbial community were investigated in juveniles of the winged pearl oyster Pteria penguin. A total of 240 pearl oysters were fed either live or spray-dried unialgal diets of the species Isochrysis zhanjiangensis and Platymonas subcordiformis at a final concentration of 150,000 cells/mL. The experiment was performed over 28 days in triplicate feeding trials under laboratory conditions. At the end of the feeding trials, the hepatopancreas and gut tissue were dissected to quantify the digestive enzymatic activity and analyze the gut bacterial community. The survival rate of the oyster juveniles in all trials was > 90 %. Moreover, the animals fed a spray-dried P. subcordiformis diet exhibited slightly higher shell growth rates. However, the mean shell height and the total wet weight were not significantly different among all experimental groups (P > 0.05). The digestive enzymes amylase, pepsin, and lipase exhibited significantly higher activity levels in oysters fed spray-dried diets than in those provided live microalgae. The different diets also provoked changes in the gut microbiota of the pearl oysters. A total of 27 phyla and 482 genera were detected within all groups examined; the Proteobacteria, Cyanobacteria, Bacteroidetes, and Spirochaetes were the dominant phyla. In general, spray-dried diets exhibited a higher number of operational taxonomic units (OTUs), Chao1, and Simpson and Shannon indices, implying the ability of these diets to promote high microbial biodiversity. Thus, these diets benefitted the maintenance of the intestinal micro-ecological balance and health. The study findings will help optimize intermediate culture technology and management of P. penguin juveniles.

Impact of mitotype diversity on metabarcoding biodiversity estimations in Insecta and Arachnida using different sample preparation strategies.

DNA barcoding and metabarcoding have been increasingly used in species delimitation and species diversity assessment, respectively, and the molecular markers used in animals are mainly derived from mitochondrial DNA. It is well known that the phenomenon of multiple mitochondrial haplotypes within the same specimen (hereafter referred to as "mitotype diversity") may have a negative impact on the proper assessment of biodiversity by metabarcoding. However, few studies have focused on the incidence of this phenomenon and its effects on metabarcoding results using different sample preparation strategies, such as mock community construction using pooled high-throughput sequencing (HTS) data, DNA-pooling and Tissue-pooling. In this study, we investigated mitotype diversity and its influence on metabarcoding based on 398 specimens from 66 species of Insecta and 82 specimens from 16 species of Arachnida by HTS of the mitochondrial cox1 gene fragment. The results revealed that mitotype diversity was common in the studied taxa and significantly increased the number of operational taxonomic units (OTUs) using the three sample preparation strategies. The results also showed that the bioinformatics pipeline based on authentic amplicon sequence variants was more reliable than the pipeline based on OTUs. Regarding the sample preparation strategies of DNA-pooling and Tissue-pooling commonly used in metabarcoding, our results revealed that their results of metabarcoding were quite similar, and the Tissue-pooling strategy was therefore preferred because of its simplicity. Our study calls for additional attention to the interference of mitotype diversity on the results of DNA metabarcoding in biodiversity assessment.

Bacterial community in Sinonovacula constricta intestine and its relationship with culture environment

Although the importance of intestinal microbes to aquaculture animals has been recognized, the intestinal bacteria of Sinonovacula constricta and its culture environment are rarely studied. In this study, high-throughput sequencing was used to explore the intestinal bacterial communities of pond water, sediment, and S. constricta intestine. Significance analysis and principal coordinates analysis (PCoA) showed that there were significant differences in bacterial communities among animals' intestine, pond water, and sediment (p < 0.05). Venn analysis showed that intestinal bacteria shared a considerable number of OTUs (operational taxonomic units) with the sediment and water. SourceTracker analysis suggested that the contribution of sediment to the intestinal bacteria of S. constricta was much larger than that of rearing water. The Kruskal-Wallis test showed that the dominant bacterial taxa differed significantly between animals' intestines and the pond environment, and each of them has a unique bacterial composition. A network diagram indicated the complex positive and negative interactions between intestinal bacteria at the OTU level. Furthermore, BugBase analysis indicated that the bacterial contribution to potential pathogens in the animals' intestines is similar to that in sediments, suggesting that sediment was the main source of potential pathogens in S. constricta intestine. This study provided a theoretical basis for environmental regulation and disease prevention of S. constricta in aquaculture. KEY POINTS: • Culture environment had a significant effect on the intestinal bacterial community in S. constricta. • Sediment was a major source of intestinal bacteria and potentially pathogenic bacteria. • Complex positive and negative interactions existed between intestinal bacteria.

Fecal Microbiota in Inflammatory Bowel Disease

Background: Diversity of microbial species is a hallmark of dysbiosis in inflammatory bowel disease (IBD). This study was undertaken to determine whether the diversity of lactobacilli and bifidobacteria, two regulatory microbial genera, is altered in patients with IBD. Methods: DNA from fecal samples of 20 healthy volunteers, 20 patients with ulcerative colitis (UC), and 25 patients with Crohn's disease (CD) was amplified by the polymerase chain reaction (PCR) for 16S ribosomal RNA gene sequences specific to genus Lactobacillus and Bifidobacterium. Real-time PCR was done to quantitate bacterial abundance. Amplified DNA was also bar coded and sequenced on the Roche 454 platform. Individual operational taxonomic units (OTUs) were taken as sequences with at least 97% similarity. Results: Abundance of Lactobacillus was significantly increased in UC compared to controls; no other difference in Lactobacillus or Bifidobacterium abundance was found between the three groups. Median reads for genus Lactobacillus was similar between control (940), UC (994), and CD (960) groups. The median number of OTUs per sample was not significantly different between controls (6), UC (5.5) and CD (7). The Shannon index of community diversity was similar between controls (median 1.12), UC (median 1.13) and CD (median 1.11). The Simpson D index was also similar between controls (median 0.393), UC (median 0.439) and CD (median 0.409). Median reads for genus Bifidobacterium was similar between control (846), UC (1052), and CD (964) groups. The median number of Bifidobacteria OTUs per sample was similar for controls (6), UC (7) and CD (8.5). The Shannon index of community diversity was similar between controls (median 0.75), UC (median 1.0) and CD (median 1.14). The Simpson D index was also similar between controls (median 0.570), UC (median 0.422) and CD (median 0.409). Conclusion: The abundance of Lactobacillus was increased in UC. Diversity of genus Lactobacillus and Bifidobacterium was not altered in either UC or CD.

Mixed planting reduces the shaping ability of legume cover crop on soil microbial community structure

Cover crop species and management are the key factors for reaping maximum benefits. Current studies lack a comprehensive assessment of the effects of cover crop species and planting patterns on soil properties, plant properties, and rhizosphere microbial communities at the full-blooming stage. A field experiment was conducted for 8 years (2011–2018) in Tianjin (fluvo-aquic soil) in China to compare various cover crops (hairy vetch, February orchid and rye) under different planting patterns (monoculture or mixed culture) in terms of cover crop biomass, soil physicochemical and biological properties, and rhizosphere microbial communities through high-throughput sequencing. The following groups were established: CK (winter fallow; the control), FO (February orchid monoculture), RY (rye monoculture), HV (hairy vetch monoculture), FOHV (February orchid–hairy vetch mixed culture), and RYHV (rye–hairy vetch mixed culture). RY had the highest biomass and nitrogen (N) uptake, and HV had the lowest biomass and highest N content. Mixed culture produced biomass higher in amount than the average biomass of monocultures of each individual species. RYHV showed a higher amount of biomass and uptake of nutrients, especially N. Cover crop planting significantly increased soil organic matter content (22.45 %–33.22 %), N levels (78.28 %–412.04 %), and available phosphate (9.70 %–45.03 %) and potassium (20.71 %–56.62 %) levels, but no significant differences in soil pH and total phosphorus content were found among the treatments. FO and HV treatments showed higher increments in soil biological properties: soil microbial biomass C (Cmic) and soil microbial biomass N (Nmic) and nematode density than the RY treatment. Mixed planting further promoted these properties, and FOHV treatment showed the highest values, which indicated improved soil properties. HV treatment significantly reduced bacterial and fungal diversity and the number of operational taxonomic units. These effects can be alleviated by mixed planting with FO and RY. Principal component analysis showed that the bacterial and fungal communities in the control were distinct from those in the cover crop treatments, and the difference was the greatest in the HV treatment. However, mixed planting with FO and RY reduced this difference between HV and CK. Structural equation model integration and analysis confirmed that the bacterial community was primarily regulated by soil physicochemical properties, whereas the fungal community was primarily regulated by plant properties. Soil biological properties affected bacterial and fungal communities, and mixed planting alleviated the impact of hairy vetch on soil microbial communities.

Influence of Gallic Acid-Containing Mouth Spray on Dental Health and Oral Microbiota of Healthy Cats-A Pilot Study.

Simple SummaryPeriodontal diseases are common dental issues in cats. Oral care supplements were used to prevent diseases and maintain oral health. Moreover, maintaining a healthy oral microbiome is crucial for oral health. Therefore, we have developed a gallic acid-containing mouth spray and studied its effect on oral microbiota and dental health in healthy cats. The results revealed that the gingival and plaque indexes were improved after 42 days of mouth spray treatment in cats. The mouth spray treatment also reduced the abundance of harmful bacterial load and supported the growth of normal oral microbiota. This preliminary study recommended that the gallic acid-containing mouth spray could be an essential oral product to improve the oral hygiene of the cats.This pilot study aimed to investigate the effects of gallic acid-containing mouth spray on oral microbiota in healthy cat subjects. Forty healthy cats were recruited and randomly allocated to the control (G1; n = 20) and treatment groups (G2; n = 20). The cats were treated with mouth spray twice daily for 42 days. The changes in the gingival index (GI) and plaque index (PI) were measured at baseline (day 0) and end of the study (42nd day). The changes in the oral microbial composition of representative animals (control, n = 9; and treatment, n = 8) were also evaluated at baseline and end of the study. Oral microbial composition was assessed by amplifying the V1–V3 region of the 16S rRNA gene from supragingival dental plaque DNA extracts. The sequences were annotated using the QIIME 2.0. The GI and PI were significantly reduced after 42 days of treatment. The deep sequencing revealed that mouth spray influenced the cats’ oral microbiome and was significantly diverse. About 20 phyla and 59 species were observed after 42 days of mouth spray usage in cats’ oral microbiota. The number of operational taxonomic units (OTUs) of post-treatment samples (PoTS) of G2 was greatly reduced compared to other samples. Further analysis revealed that mouth spray acts substantially against Desulfomicrobium orale, one of the known pathogens in periodontal disease. The mouth spray efficiently reduced the growth of 22 species and uprooted 17 species. Moreover, the mouth spray supported the growth of normal oral microbiota, including Moraxella and Neisseria species. The preliminary study suggested that the gallic acids-containing mouth spray could be an essential oral product to improve the oral hygiene of the cats. Moreover, further studies are needed to confirm the beneficial effect of mouth spray on cats.

Effects of high-grain diet feeding on mucosa-associated bacterial community and gene expression of tight junction proteins and inflammatory cytokines in the small intestine of dairy cattle

The objective of this study was to investigate changes in the composition of mucosa-associated bacterial community, the morphology of the small intestinal epithelia, and the gene expressions of junction proteins and inflammatory cytokines in the small intestines of dairy cattle fed a high-grain (HG) diet. A total of 12 ruminally cannulated Holstein cows in mid-lactation were randomly fed either a conventional (CON) diet (40% concentrate, dry matter basis) or an HG diet (60% concentrate, dry matter basis) for 4 wk. At the end of the feeding trial, all the cows were slaughtered and then examined for changes in the small intestinal mucosa-associated bacterial communities using 16S full-length amplicon sequencing. Furthermore, the gene expression of tight junction proteins and inflammatory cytokines in the small intestinal epithelium were studied using real-time quantitative PCR. The results of nonmetric multidimensional scaling plots showed that an HG diet altered the composition of mucosa-associated bacterial communities in the jejunum and ileum. The HG feeding only increased the numbers of operational taxonomic units in the mucosa-associated bacterial community in the jejunum. At the genus level, the HG diet increased the abundance of uncultured Succinivibrionaceae and Lachnospiraceae incertae sedis in the duodenal mucosa, whereas the proportions of Veillonella and Selenomonas increased in the jejunal mucosa. Compared with the CON group, the proportions of Acetitomaculum in both the jejunal and the ileal mucosa were higher in the HG group. Analysis via PICRUSt2 (version 2.2.0-b) suggested that the HG diet increased the abundance of genes related to biodegradation of xenobiotics in the jejunal mucosa and the abundance of genes related to immune disease in the ileal mucosa. Additionally, the group fed an HG diet had higher concentrations of lipopolysaccharides in the jejunal and ileal digesta. The HG feeding caused a downregulation of the mRNA expression of occludin and ZO-1 in the jejunal epithelium, as well as of claudin-1, claudin-4, and ZO-1 in the ileal epithelium. Moreover, the HG diet caused an increase in the mRNA expression of IL-1β, IL-2, and IFN-γ in the jejunal epithelium, but a higher expression of IL-2 and IFN-γ in the ileal epithelium. Correlation analysis revealed that the alteration of lipopolysaccharide levels and mucosa-associated bacterial community might partly contribute to changes in the expression of the epithelial cytokines in the jejunum and ileum during HG feeding. These findings suggest that microbiota residing in the small intestine provide essential health benefits to host dairy cattle.

Unraveling Nitrogen Fixing Potential of Endophytic Diazotrophs of Different Saccharum Species for Sustainable Sugarcane Growth.

Sugarcane (Saccharum officinarum L.) is one of the world’s highly significant commercial crops. The amounts of synthetic nitrogen (N2) fertilizer required to grow the sugarcane plant at its initial growth stages are higher, which increases the production costs and adverse environmental consequences globally. To combat this issue, sustainable environmental and economic concerns among researchers are necessary. The endophytic diazotrophs can offer significant amounts of nitrogen to crops through the biological nitrogen fixation mediated nif gene. The nifH gene is the most extensively utilized molecular marker in nature for studying N2 fixing microbiomes. The present research intended to determine the existence of novel endophytic diazotrophs through culturable and unculturable bacterial communities (EDBCs). The EDBCs of different tissues (root, stem, and leaf) of five sugarcane cultivars (Saccharum officinarum L. cv. Badila, S. barberi Jesw.cv Pansahi, S. robustum, S. spontaneum, and S. sinense Roxb.cv Uba) were isolated and molecularly characterized to evaluate N2 fixation ability. The diversity of EDBCs was observed based on nifH gene Illumina MiSeq sequencing and a culturable approach. In this study, 319766 operational taxonomic units (OTUs) were identified from 15 samples. The minimum number of OTUs was recorded in leaf tissues of S. robustum and maximum reads in root tissues of S. spontaneum. These data were assessed to ascertain the structure, diversity, abundance, and relationship between the microbial community. A total of 40 bacterial families with 58 genera were detected in different sugarcane species. Bacterial communities exhibited substantially different alpha and beta diversity. In total, 16 out of 20 genera showed potent N2-fixation in sugarcane and other crops. According to principal component analysis (PCA) and hierarchical clustering (Bray–Curtis dis) evaluation of OTUs, bacterial microbiomes associated with root tissues differed significantly from stem and leaf tissues of sugarcane. Significant differences often were observed in EDBCs among the sugarcane tissues. We tracked and validated the plethora of individual phylum strains and assessed their nitrogenase activity with a culture-dependent technique. The current work illustrated the significant and novel results of many uncharted endophytic microbial communities in different tissues of sugarcane species, which provides an experimental system to evaluate the biological nitrogen fixation (BNF) mechanism in sugarcane. The novel endophytic microbial communities with N2-fixation ability play a remarkable and promising role in sustainable agriculture production.

Long‐term ground cover affects soil bacterial community and carbon metabolism in the Loess Plateau, China

AbstractFarmland mulching can maintain soil nutrients, which plays a positive role in agricultural planting in the arid area. However, the composition of the soil microbial community and the C cycle involved is unclear under farmland mulching. Based on the Changwu Agro‐Ecological Experiment Station, this study set up a long‐term positioning experiment to explore the effect on soil bacterial community structure and C metabolism capacity. In this study, we include five treatments: control uncovered (CK), plastic film mulching (PF), high amount of straw mulching carried out in July, August, and September every year (St90), low amount of straw mulch throughout the growth period (S45), and high amount of straw cover throughout the growth period (S90). We combined Illumina MiSeq sequencing and Biolog‐ECO technology to analyze the functional characterization of soil bacterial community composition in terms of C source metabolism. The results indicated that the soil bacteria showed a high degree of epistatic clustering, and the operational taxonomic unit numbers of soil bacteria decrease as St90, S45, PF, CK, and S90. Redundancy analysis showed that soil available P, NH4+–N, soil moisture content were the main environmental factors affecting bacterial community composition. Proteobacteria, Acidobacteria, and Actinobacteria are the main dominant flora in this area. Soil bacterial C metabolism was highest under PF treatment. Structural equation modeling (SEM) shows that surface cover has direct and indirect effects on bacterial C metabolism capacity and diversity through soil physicochemical properties. Reasonable mulching methods have a positive effect on the sustainable development of agro‐ecosystems in arid areas.