“Breeding on Mountains” Resulted in the Reorganization of Endophytic Fungi in Asexually Propagated Plants (Ligusticum chuanxiong Hort.)

“Breeding on mountains, cultivation in dam areas” is a unique propagation method for the vegetatively propagated plant Ligusticum chuanxiong, including two transplants between the mountain and the dam area. It is well known that the environment can influence the endophytic community structure of plants. However, the change of host endophytic flora caused by transplanting in different places and its influence on asexual reproduction are still poorly understood. We carried out three cycles of cultivation experiments on L. chuanxiong and collected stem nodes (LZ), immature rhizomes (PX), medicinal rhizomes (CX), and rhizosphere. High-throughput sequencing was performed to analyze the endophytic fungi in all samples. We observed that the diversity and richness of endophytic fungi in L. chuanxiong increased as a result of transplanting cultivation from dam areas to mountains. Local transplantation caused minor changes in the endophytic fungus structure of L. chuanxiong, while remote transplantation caused significant changes. Compared with LZ after breeding in the dam area, the LZ after breeding on mountains has more abundant Gibberella, Phoma, Pericona, Paraphoma, and Neocosmospora. The regular pattern of the relative abundance of endophytic fungi is consistent with that of the fungus in the soil, while there are also some cases that the relative abundance of endophytic fungi is the opposite of that of soil fungi. In addition, there is a significant correlation among certain kinds of endophytic fungi whether in the soil or the plants. We have isolated more gibberellin-producing and auxin-producing fungi in the LZ cultivated in the mountains than that in the LZ cultivated in the dam area. The results of pot experiments showed that the three fungi isolated from LZ cultivated in mountainous areas can promote the development of shoots, stem nodes, and internodes of LZ, and increase the activity of plant peroxidase, catalase, phenylalanine ammonia lyase, and other enzymes. We can conclude that transplantation leads to the recombination of the host endophytic fungus, the more significant the difference in the environment is, the greater the reorganization caused by transplanting. Reorganization is determined by the soil environment, hosts, and the interaction of microorganisms. Remote transplantation is a crucial opportunity to reshuffle the micro-ecological structure of the asexual reproduction of plants, and regulate the growth, development, and resistance of plants, and prevent germplasm degradation caused by asexual reproduction.

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Analysis of the relationship between caecal flora difference and production performance of two rabbit species by high-throughput sequencing

Czech Journal of Animal Science ◽

10.17221/225/2020-cjas ◽

2021 ◽

Author(s):

Zhiqiang Guo ◽

Bin Wang ◽

Jingzhi Lu ◽

Congyan Li ◽

Liangde Kuang ◽

...

Keyword(s):

High Throughput ◽

Relative Abundance ◽

High Throughput Sequencing ◽

Average Daily Gain ◽

Intestinal Flora ◽

Nutritional Composition ◽

Production Performance ◽

Light Cycle ◽

The Difference ◽

The Relationship

The purpose of this experiment is to study the relationship between the difference in production performance between Sichuan White (SC) rabbits and New Zealand (NZL) rabbits and the diversity of caecal flora. Twelve pregnant SC rabbits and 12 NZL female rabbits were selected for this experiment. After delivery, the young rabbits were divided into two groups according to breeds, each group had 30 replicates, and each replicate had one rabbit. During the experiments, these rabbits were kept in the same room, and the temperature in the room was controlled at 12–25 °C, with a 16-hour light cycle every 24 hours. The nutritional composition of the feed and other environmental conditions were consistent. On the 59<sup>th</sup> day of the experiment, the caecum contents of the two groups of young rabbits were collected. The results showed that the survival rate of the SC rabbit group was higher than that of the NZL rabbit group, and the diarrhoea rate and average daily gain were lower than those of the NZL rabbit group (P < 0.05). The results of high-throughput sequencing of the 16S gene showed that compared with the NZL rabbit group, the relative abundance of Bacteroides increased, and the abundance of harmful flora Verrucomicrobia and Proteobacteria decreased (P < 0.05). Functional analysis of the microflora showed that the relative abundance of carbohydrate metabolism genes in the SC rabbit group was higher than in the NZL rabbit group. In conclusion, compared with the NZL rabbits, the SC rabbits have a more optimized intestinal flora structure and lower abundance of harmful bacteria. Moreover, the intestinal health level of SC rabbits is improved, and the tolerance to roughage of SC rabbits is increased.

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Taxonomic and Functional Characteristics of the Gill and Gastrointestinal Microbiota and Its Correlation with Intestinal Metabolites in NEW GIFT Strain of Farmed Adult Nile Tilapia (Oreochromis niloticus)

Microorganisms ◽

10.3390/microorganisms9030617 ◽

2021 ◽

Vol 9 (3) ◽

pp. 617

Author(s):

Zhenbing Wu ◽

Qianqian Zhang ◽

Yaoyao Lin ◽

Jingwen Hao ◽

Shuyi Wang ◽

...

Keyword(s):

Relative Abundance ◽

Oreochromis Niloticus ◽

Nile Tilapia ◽

High Throughput Sequencing ◽

Gas Chromatography Mass Spectrometry ◽

Gastrointestinal Mucosa ◽

Gastrointestinal Microbiota ◽

Linear Discriminant ◽

Intestinal Microbes ◽

Nile Tilapia Oreochromis Niloticus

The gill and gastrointestinal tract are primary entry routes for pathogens. The symbiotic microbiota are essential to the health, nutrition and disease of fish. Though the intestinal microbiota of Nile tilapia (Oreochromis niloticus) has been extensively studied, information on the mucosa-associated microbiota of this species, especially the gill and gastrointestinal mucosa-associated microbiota, is lacking. This study aimed to characterize the gill and gastrointestinal mucosa- and digesta-associated microbiota, as well as the intestinal metabolite profiles in the New Genetically Improved Farmed Tilapia (NEW GIFT) strain of farmed adult Nile tilapia by high-throughput sequencing and gas chromatography/mass spectrometry metabolomics. The diversity, structure, composition, and predicted function of gastrointestinal microbiota were significantly different across gastrointestinal regions and sample types (Welch t-test; p < 0.05). By comparing the mucosa- and digesta-associated microbiota, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that Pelomonas, Ralstoniapickettii, Comamonadaceae, and Staphylococcus were significantly enriched in the mucosa-associated microbiota, whereas many bacterial taxa were significantly enriched in the digesta-associated microbiota, including Chitinophagaceae, Cetobacterium, CandidatusCompetibacter, Methyloparacoccus, and chloroplast (LDA score > 3.5). Furthermore, Undibacterium, Escherichia–Shigella, Paeniclostridium, and Cetobacterium were dominant in the intestinal contents and mucosae, whereas Sphingomonasaquatilis and Roseomonasgilardii were commonly found in the gill and stomach mucosae. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) analysis revealed that the predictive function of digesta-associated microbiota significantly differed from that of mucosa-associated microbiota (R = 0.8152, p = 0.0001). In addition, our results showed a significant interdependence between specific intestinal microbes and metabolites. Notably, the relative abundance values of several potentially beneficial microbes, including Undibacterium, Crenothrix, and Cetobacterium, were positively correlated with most intestinal metabolites, whereas the relative abundance values of some potential opportunistic pathogens, including Acinetobacter, Mycobacterium, Escherichia–Shigella, Paeniclostridium, Aeromonas, and Clostridiumsensustricto 1, were negatively correlated with most intestinal metabolites. This study revealed the characteristics of gill and gastrointestinal mucosa-associated and digesta-associated microbiota of farmed Nile tilapia and identified a close correlation between intestinal microbes and metabolites. The results serve as a basis for the effective application of targeted probiotics or prebiotics in the diet to regulate the nutrition and health of farmed tilapia.

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Urbanization pressures alter tree rhizosphere microbiomes

Scientific Reports ◽

10.1038/s41598-021-88839-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Carl L. Rosier ◽

Shawn W. Polson ◽

Vincent D’Amico ◽

Jinjun Kan ◽

Tara L. E. Trammell

Keyword(s):

Organic Matter ◽

Relative Abundance ◽

Tree Species ◽

High Throughput Sequencing ◽

Regional Climate ◽

Keystone Species ◽

Fagus Grandifolia ◽

Yellow Poplar ◽

Individual Tree ◽

Structural Formation

AbstractThe soil microbial community (SMC) provides critical ecosystem services including organic matter decomposition, soil structural formation, and nutrient cycling. Studies suggest plants, specifically trees, act as soil keystone species controlling SMC structure via multiple mechanisms (e.g., litter chemistry, root exudates, and canopy alteration of precipitation). Tree influence on SMC is shaped by local/regional climate effects on forested environments and the connection of forests to surrounding landscapes (e.g., urbanization). Urban soils offer an ideal analog to assess the influence of environmental conditions versus plant species-specific controls on SMC. We used next generation high throughput sequencing to characterize the SMC of specific tree species (Fagus grandifolia [beech] vs Liriodendron tulipifera [yellow poplar]) across an urban–rural gradient. Results indicate SMC dissimilarity within rural forests suggests the SMC is unique to individual tree species. However, greater urbanization pressure increased SMC similarity between tree species. Relative abundance, species richness, and evenness suggest that increases in similarity within urban forests is not the result of biodiversity loss, but rather due to greater overlap of shared taxa. Evaluation of soil chemistry across the rural–urban gradient indicate pH, Ca+, and organic matter are largely responsible for driving relative abundance of specific SMC members.

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New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

Microorganisms ◽

10.3390/microorganisms9030659 ◽

2021 ◽

Vol 9 (3) ◽

pp. 659

Author(s):

Elias Asimakis ◽

Panagiota Stathopoulou ◽

Apostolis Sapounas ◽

Kanjana Khaeso ◽

Costas Batargias ◽

...

Keyword(s):

Relative Abundance ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Mutual Exclusion ◽

Bacterial Composition ◽

Operational Taxonomic Units ◽

Host Diet ◽

Dominant Bacteria ◽

High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

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Seasonal Variation Characteristics of Bacteria and Fungi in PM2.5 in Typical Basin Cities of Xi’an and Linfen, China

Atmosphere ◽

10.3390/atmos12070809 ◽

2021 ◽

Vol 12 (7) ◽

pp. 809

Author(s):

Sen Wang ◽

Wanyu Liu ◽

Jun Li ◽

Haotian Sun ◽

Yali Qian ◽

...

Keyword(s):

Seasonal Variation ◽

Relative Abundance ◽

Pathogenic Bacteria ◽

High Throughput Sequencing ◽

Fine Particulate Matter ◽

Ecological Functions ◽

Factors Affecting ◽

Bacterial Phyla ◽

Variation Characteristics ◽

Bacteria And Fungi

Microorganisms existing in airborne fine particulate matter (PM2.5) have key implications in biogeochemical cycling and human health. In this study, PM2.5 samples, collected in the typical basin cities of Xi’an and Linfen, China, were analyzed through high-throughput sequencing to understand microbial seasonal variation characteristics and ecological functions. For bacteria, the highest richness and diversity were identified in autumn. The bacterial phyla were dominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Metabolism was the most abundant pathway, with the highest relative abundance found in autumn. Pathogenic bacteria (Pseudomonas, Acinetobacter, Serratia, and Delftia) were positively correlated with most disease-related pathways. Besides, C cycling dominated in spring and summer, while N cycling dominated in autumn and winter. The relative abundance of S cycling was highest during winter in Linfen. For fungi, the highest richness was found in summer. Basidiomycota and Ascomycota mainly constituted the fungal phyla. Moreover, temperature (T) and sulfur dioxide (SO2) in Xi’an, and T, SO2, and nitrogen dioxide (NO2) in Linfen were the key factors affecting microbial community structures, which were associated with different pollution characteristics in Xi’an and Linfen. Overall, these results provide an important reference for the research into airborne microbial seasonal variations, along with their ecological functions and health impacts.

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Dynamics of Diversity and Abundance of Sulfonamide Resistant Bacteria in a Silt Loam Soil Fertilized by Compost

Antibiotics ◽

10.3390/antibiotics10060699 ◽

2021 ◽

Vol 10 (6) ◽

pp. 699

Author(s):

Hui Han ◽

Mohan Bai ◽

Yanting Chen ◽

Yali Gong ◽

Ming Wu ◽

...

Keyword(s):

High Throughput ◽

Relative Abundance ◽

High Throughput Sequencing ◽

Resistant Bacteria ◽

Arable Soils ◽

Soil Bacterial Communities ◽

Sulfonamide Resistance ◽

Loam Soil ◽

Abundance And Diversity ◽

Sulfonamide Resistance Genes

Although composting is effective in deactivating antibiotic substances in manure, the influence of compost fertilization on the occurrence and dissemination of antibiotic resistance in arable soils remains to be controversial. Herein, the abundance and diversity of two sulfonamide resistance genes (sul1 and sul2) in soil fertilized by compost spiked with two concentrations of sulfadiazine (1 and 10 mg kg−1) were studied intensively by qPCR and high throughput sequencing based on a two-month microcosm experiment. The concentration of sulfadiazine decreased rapidly after spiking from 25% at Day 1 to less than 2.7% at Day 60. Relative abundance of both sul1 and sul2 were significantly higher in soil amended with compost than the non-amended control at Day 1 and slightly decreased with incubation time except for sul2 in the S10 treatment. Soil bacterial communities were transiently shifted by compost fertilization regardless of the presence of sulfadiazine. Relative abundance of genera in three hubs positively interlinked with sul1 and sul2 were significantly higher in compost treated soil than the control at Day 1, 7 and 21, but not at Day 60. High throughput sequencing analyses revealed that most detected (>67% in relative abundance) sul1 and sul2 genotypes sharing >99% similarity with those found in gammaproteobacterial pathogens frequently were commonly present in compost and soil. These results indicated that compost fertilization might increase the abundance rather than diversity of sulfadiazine-resistant populations in soil, which may be facilitated by the presence of sulfadiazine.

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Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

Applied and Environmental Microbiology ◽

10.1128/aem.00560-16 ◽

2016 ◽

Vol 82 (15) ◽

pp. 4757-4766 ◽

Cited By ~ 55

Author(s):

Caterina R. Giner ◽

Irene Forn ◽

Sarah Romac ◽

Ramiro Logares ◽

Colomban de Vargas ◽

...

Keyword(s):

Microbial Diversity ◽

High Throughput ◽

Relative Abundance ◽

Ribosomal Dna ◽

18S Rdna ◽

High Throughput Sequencing ◽

454 Sequencing ◽

Epifluorescence Microscopy ◽

Environmental Sequencing

ABSTRACTHigh-throughput sequencing (HTS) is revolutionizing environmental surveys of microbial diversity in the three domains of life by providing detailed information on which taxa are present in microbial assemblages. However, it is still unclear how the relative abundance of specific taxa gathered by HTS correlates with cell abundances. Here, we quantified the relative cell abundance of 6 picoeukaryotic taxa in 13 planktonic samples from 6 European coastal sites using epifluorescence microscopy on tyramide signal amplification-fluorescencein situhybridization preparations. These relative abundance values were then compared with HTS data obtained in three separate molecular surveys: 454 sequencing of the V4 region of the 18S ribosomal DNA (rDNA) using DNA and RNA extracts (DNA-V4 and cDNA-V4) and Illumina sequencing of the V9 region (cDNA-V9). The microscopic and molecular signals were generally correlated, indicating that a relative increase in specific 18S rDNA was the result of a large proportion of cells in the given taxa. Despite these positive correlations, the slopes often deviated from 1, precluding a direct translation of sequences to cells. Our data highlighted clear differences depending on the nucleic acid template or the 18S rDNA region targeted. Thus, the molecular signal obtained using cDNA templates was always closer to relative cell abundances, while the V4 and V9 regions gave better results depending on the taxa. Our data support the quantitative use of HTS data but warn about considering it as a direct proxy of cell abundances.IMPORTANCEDirect studies on marine picoeukaryotes by epifluorescence microscopy are problematic due to the lack of morphological features and due to the limited number and poor resolution of specific phylogenetic probes used in fluorescencein situhybridization (FISH) routines. As a consequence, there is an increasing use of molecular methods, including high-throughput sequencing (HTS), to study marine microbial diversity. HTS can provide a detailed picture of the taxa present in a community and can reveal diversity not evident using other methods, but it is still unclear what the meaning of the sequence abundance in a given taxon is. Our aim is to investigate the correspondence between the relative HTS signal and relative cell abundances in selected picoeukaryotic taxa. Environmental sequencing provides reasonable estimates of the relative abundance of specific taxa. Better results are obtained when using RNA extracts as the templates, while the region of 18S ribosomal DNA had different influences depending on the taxa assayed.

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Isolation of Endophytic Fungi QPS 05 from Quercus phillyraeoides A. Gray and Its Potential for α-Glucosidase Inhibitory Activity

Jurnal Kimia Terapan Indonesia ◽

10.14203/jkti.v20i1.372 ◽

2018 ◽

Vol 20 (1) ◽

pp. 1-7

Author(s):

Anastasia Wheni Indrianingsih ◽

Amalia Indah Prihantini ◽

Sanro Tachibana

Keyword(s):

Fatty Acids ◽

Endophytic Fungi ◽

Inhibitory Activity ◽

Endophytic Fungus ◽

Inhibitory Concentration ◽

Life Cycles ◽

Ic50 Values ◽

Quercus Phillyraeoides ◽

Alternaria Sp ◽

Harmful Effects

AbstractEndophytic fungi are the microorganisms that spend all or part of their life cycles within plant tissue without causing harmful effects on the plant. In this study, 14 endophytic fungus from Quercus phillyraeoides A. Gray were isolated. Alternaria sp. QPS 05, an endophytic fungi which was isolated from the stem of Q. phillyraeoides A. Gray showed the highest α-glucosidase inhibitory activity. Further separation of ethyl acetate extract from the fungus led to the isolation of active substance from hexane-soluble fraction which give fatty acids mixture consist of palmitic acid, oleic acid, linoleic acid and linolenic acid (1) strong inhibitory activity against α-glucosidase. Isolated fatty acids (1) had inhibitory concentration (IC50) values against Saccharomyces cerevisiae was 12.10 μg/mL. The results of the present study showed that endophytic fungus from Alternaria sp. QPS 05 potentially contained a rich source of natural antidiabetic medicine.

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Comparative Analysis of the Fecal Bacterial Microbiota of Wintering Whooper Swans (Cygnus Cygnus)

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.670645 ◽

2021 ◽

Vol 8 ◽

Author(s):

Wenxia Wang ◽

Songlin Huang ◽

Liangliang Yang ◽

Guogang Zhang

Keyword(s):

Intestinal Microbiota ◽

Relative Abundance ◽

High Throughput Sequencing ◽

The Body ◽

16S Rrna Genes ◽

Rrna Genes ◽

Illumina Hiseq ◽

Linear Discriminant ◽

Bacterial Microbiota ◽

And Control

There are many and diverse intestinal microbiota, and they are closely related to various physiological functions of the body. They directly participate in the host's food digestion, nutrient absorption, energy metabolism, immune response, and many other physiological activities and are also related to the occurrence of many diseases. The intestinal microbiota are extremely important for maintaining normal physical health. In order to explore the composition and differences of the intestinal microbiota of whooper swans in different wintering areas, we collected fecal samples of whooper swans in Sanmenxia, Henan, and Rongcheng, Shandong, and we used the Illumina HiSeq platform to perform high-throughput sequencing of bacterial 16S rRNA genes. Comparison between Sanmenxia and Rongcheng showed no significant differences in ACE, Chao 1, Simpson, and Shannon indices (p > 0.05). Beta diversity results showed significant differences in bacterial communities between two groups [analysis of similarity (ANOSIM): R = 0.80, p = 0.011]. Linear discriminant analysis effect size (LEfSe) analysis showed that at the phylum level, the relative abundance of Actinobacteria was significantly higher in Sanmenxia whooper swans than Rongcheng whooper swans. At the genus level, the amount of Psychrobacter and Carnobacterium in Sanmenxia was significantly higher in Rongcheng, while the relative abundance Catellicoccus and Lactobacillus was significantly higher in Rongcheng than in Sanmenxia. This study analyzed the composition, characteristics, and differences of the intestinal microbiota of the whooper swans in different wintering environments and provided theoretical support for further exploring the relationship between the intestinal microbiota of the whooper swans and the external environment. And it played an important role in the overwintering physiology and ecology, population management, and epidemic prevention and control of whooper swans.

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Comparison of Oral Hygiene Status and Relative Abundance of Periodontal Pathogens Between Individuals With and Without Intellectual Disabilities: a Cross-Sectional Study

10.21203/rs.3.rs-49931/v1 ◽

2020 ◽

Author(s):

Yuki Oda ◽

Chiaki Furutani ◽

Reo Kawano ◽

Jumpei Murakami ◽

Yuika Mizota ◽

...

Keyword(s):

Periodontal Disease ◽

Relative Abundance ◽

Outpatient Clinic ◽

High Throughput Sequencing ◽

Analysis Of Covariance ◽

University Hospital ◽

Permanent Teeth ◽

Control Group ◽

Periodontal Pathogens ◽

Significant Difference

Abstract Background: Studies have reported a high prevalence of periodontal disease in individuals with intellectual disability (ID). The aim of this study was to compare the relative abundance of periodontal pathogens (red, orange, yellow, purple, and green complexes) between individuals with ID and healthy controls.Methods: Of the 31 subjects enrolled in this study, 16 with severe ID were selected from the outpatient clinic of the Special Care Dentistry of Hiroshima University Hospital, and 14 healthy subjects were selected from the outpatient clinic of another department at the same hospital. Dental plaque was sampled after oral examination. Decayed, missing, and filled permanent teeth (DMFT) counts were obtained and periodontal measurements were taken using the papillary-marginal-attached (PMA) index, plaque index (PI), gingival index (GI), and probing depth (PD). Gene sequencing (16S rRNA) was performed for each sample using next-generation high-throughput sequencing methods. The relative abundance of the periodontal pathogens and the clinical parameters were compared. An unpaired t-test was used to compare the oral health status in both groups and analysis of covariance was performed to compare the relative abundance of each pathogen.Results: No statistically significant difference in DMFT was observed between the two groups. However, significant differences in the median PMA index, PI, and GI were noted between the groups (P < 0.0001). In addition, the mean PD in the ID group was significantly higher than that in the control group (P < 0.0001). The relative abundances of Tannerella spp. and Treponema spp. were significantly higher in the ID group when compared to the control group at the genus level (P = 0.0383 and 0.0432, respectively); alternatively, the relative abundance of Porphyromonas spp. was significantly lower in the ID group (P < 0.0001).Conclusions: The PMA index, PI, GI, and PD were significantly lower in the ID group than in the control group. On the other hand, no significant difference in DMFT was observed between the two groups. Furthermore, our findings indicate that Tannerella forsythia might be more closely associated with periodontal disease than Porphyromonas gingivalis in individuals with ID.

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