Microbial Clusters Research Articles

A single amino acid residue controls acyltransferase activity in a polyketide synthase from Toxoplasma gondii

SummaryType I polyketide synthases (PKSs) are multidomain, multimodule enzymes capable of producing complex polyketide metabolites. These modules contain an acyltransferase (AT) domain, which selects acyl-CoA substrates to be incorporated into the metabolite scaffold. Herein, we reveal the sequences of three AT domains from a polyketide synthase (TgPKS2) from the apicomplexan parasite Toxoplasma gondii. Phylogenic analysis indicates these ATs (AT1, AT2, and AT3) are distinct from domains in well-characterized microbial biosynthetic gene clusters. Biochemical investigations revealed that AT1 and AT2 hydrolyze malonyl-CoA but the terminal AT3 domain is non-functional. We further identify an “on-off switch” residue that controls activity such that a single amino acid change in AT3 confers hydrolysis activity while the analogous mutation in AT2 eliminates activity. This biochemical analysis of AT domains from an apicomplexan PKS lays the foundation for further molecular and structural studies on PKSs from T. gondii and other protists.

Impacts of food waste to sludge ratios on microbial dynamics and functional traits in thermophilic digesters

A self-stabilizing microbial community lays the foundation of the efficient biochemical reactions of the anaerobic digestion (AD) process. Despite extensive profiling of microbial community dynamics under varying operating parameters, the effects of food waste (FW) to feeding sewage sludge (FSS) ratios on the microbial assembly, functional traits, and syntrophic interspecies interactions in thermophilic microbial consortia remain poorly understood. Here, we investigated the long-term impacts of the FW: FSS ratio on the thermophilic AD microbiome using genome-centric metagenomics. Both the short reads (SRs) assembly, and the iterative hybrid assembly (IHA) of SRs and nanopore long reads (LRs) were used to reconstruct metagenome-assembled genomes (MAGs) and four microbial clusters were identified, demonstrating different microbial dynamics patterns in response to varying FW:FSS ratios. Cluster C1-C3 were comprised of full functional members with genetic potentials in fulfilling empirical AD biochemical reactions, wherein, syntrophic decarboxylating acetogens could interact with methanogens, and some microbes could be energized by the electron bifurcation mechanism to drive thermodynamics unfavorable reactions. We found the co-existence of both acetogenic and hydrogenotrophic methanogens in the AD microbiome, and they altered their trophic groups to scavenge the methanogenic substrates in ensuring the methane generation in digesters with different FW:FSS ratios. Another interesting observation was that two phylogenetically close Thermotogota species showed a possible strong competition on carbon source inferred by the nearly complete genetic overlap of their relevant pathways.

Intake of Natural, Unprocessed Tiger Nuts (Cyperus esculentus L.) Drink Significantly Favors Intestinal Beneficial Bacteria in a Short Period of Time

Horchata is a natural drink obtained from tiger nut tubers (Cyperus esculentus L.). It has a pleasant milky aspect and nutty flavor; some health benefits have been traditionally attributed to it. This study evaluated the effects of an unprocessed horchata drink on the gut microbiota of healthy adult volunteers (n = 31) who consumed 300 mL of natural, unprocessed horchata with no added sugar daily for 3 days. Although there were no apparent microbial profile changes induced by horchata consumption in the studied population, differences could be determined when volunteers were segmented by microbial clusters. Three distinctive enterogroups were identified previous to consuming horchata, respectively characterized by the relative abundances of Blautia and Lachnospira (B1), Bacteroides (B2) and Ruminococcus and Bifidobacterium (B3). After consuming horchata, samples of all volunteers were grouped into two clusters, one enriched in Akkermansia, Christenellaceae and Clostridiales (A1) and the other with a remarkable presence of Faecalibacterium, Bifidobacterium and Lachnospira (A2). Interestingly, the impact of horchata was dependent on the previous microbiome of each individual, and its effect yielded microbial profiles associated with butyrate production, which are typical of a Mediterranean or vegetable/fiber-rich diet and could be related to the presence of high amylose starch and polyphenols.

Microbial metabolites: cause or consequence in gastrointestinal disease?

Systems biology studies have established that changes in gastrointestinal microbiome composition and function can adversely impact host physiology. Notable diseases synonymously associated with dysbiosis include inflammatory bowel diseases, cancer, metabolic disorders, and opportunistic and recurrent pathogen infections. However, there is a scarcity of mechanistic data that advances our understanding of taxonomic correlations with pathophysiological host-microbiome interactions. Generally, to survive a hostile gut environment, microbes are highly metabolically active and produce trans-kingdom signaling molecules to interact with competing microorganisms and the host. These specialized metabolites likely play important homeostatic roles, and identifying disease-specific taxa and their effector pathways can provide better strategies for diagnosis, treatment, and prevention, as well as the discovery of innovative therapeutics. The signaling role of microbial biotransformation products such as bile acids, short-chain fatty acids, polysaccharides, and dietary tryptophan is increasingly recognized, but little is known about the identity and function of metabolites that are synthesized by microbial biosynthetic gene clusters, including ribosomally synthesized and posttranslationally modified peptides (RiPPs), nonribosomal peptides (NRPs), polyketides (PKs), PK-NRP hybrids, and terpenes. Here we consider how bioactive natural products directly encoded by the human microbiome can contribute to the pathophysiology of gastrointestinal disease, cancer, autoimmune, antimicrobial-resistant bacterial and viral infections (including COVID-19). We also present strategies used to discover these compounds and the biological activities they exhibit, with consideration of therapeutic interventions that could emerge from understanding molecular causation in gut microbiome research.

Development of the gut microbiota in healthy children in the first ten years of life: associations with internalizing and externalizing behavior

ABSTRACT Background Increasing evidence indicates that psychopathological disorders are associated with the gut microbiota. However, data are largely lacking from long-term longitudinal birth cohorts, especially those comprising low-risk healthy individuals. Therefore, this study aims to describe gut microbiota development in healthy children from birth till age 10 years, as well as to investigate potential associations with internalizing and externalizing behavior. Results Fecal microbial composition of participants in an ongoing longitudinal study (N = 193) was analyzed at 1, 3 and 4 months, and 6 and 10 years of age by 16S ribosomal RNA gene sequencing. Based on these data, three clusters were identified in infancy, two of which were predominated by Bifidobacterium. In childhood, four clusters were observed, two of which increased in prevalence with age. One of the childhood clusters, similar to an enterotype, was highly enriched in genus-level taxon Prevotella_9. Breastfeeding had marked associations with microbiota composition up till age 10, implying an extended role in shaping gut microbial ecology. Microbial clusters were not associated with behavior. However, Prevotella_9 in childhood was positively related to mother-reported externalizing behavior at age 10; this was validated in child reports. Conclusions This study validated previous findings on Bifidobacterium-enriched and -depleted clusters in infancy. Importantly, it also mapped continued development of gut microbiota in middle childhood. Novel associations between gut microbial composition in the first 10 years of life (especially Prevotella_9), and externalizing behavior at age 10 were found. Replications in other cohorts, as well as follow-up assessments, will help determine the significance of these findings.

Key microbial clusters and environmental factors affecting the removal of antibiotics in an engineered anaerobic digestion system

To identify the key microbial clusters and influencing factors involved in antibiotic removal from engineered anaerobic digestion (AD) systems, the dynamic characteristics of antibiotics, physiochemical factors, microbial communities and functional genes were investigated by 16S rRNA and metagenome sequencing. The results showed that antibiotic removal occurred mainly in the first 21 days, and sulfonamides had the highest removal rate. The key microbial clusters related to the biodegradation of antibiotics consisted mainly of Firmicutes and Bacteroidetes. The key enzymes consisted of deaminases, peptidases, C-N ligases, decarboxylases and alkyl-aryl transferases. Structural equation modelling indicated that low concentrations of propionic acid promoted the biodegradation activities of key microbial clusters in the first 21 days, but their activities were inhibited by the accumulated propionic acid after 21 days. Thus, propionic acid should be regulated in engineered AD systems to prevent the adverse effect of acid inhibition on antibiotic-degrading bacteria.

Rumen Microbial Cluster Identification and its Influence on Rumen Metabolites and Growth Performance of Young Goats

Rumen Microbial Cluster Identification and its Influence on Rumen Metabolites and Growth Performance of Young Goats

The microbial gbu gene cluster links cardiovascular disease risk associated with red meat consumption to microbiota L-carnitine catabolism.

The heightened cardiovascular disease (CVD) risk observed with omnivores is thought to be linked, in part, to gut microbiota-dependent generation trimethylamine-N-oxide (TMAO) from L-carnitine, a nutrient abundant in red meat. Gut microbial transformation of L-carnitine into trimethylamine (TMA), the precursor of TMAO, occurs via the intermediate γ-butyrobetaine (γBB). However, the relationship between γBB, red meat ingestion and CVD risks, as well as the gut microbial genes responsible for the transformation of γBB to TMA, are unclear. Here we show plasma γBB levels in individuals from a clinical cohort (n=2,918) are strongly associated with incident CVD event risks. Culture of human fecal samples and microbial transplantation studies in gnotobiotic mice with defined synthetic communities showed that the introduction of Emergencia timonensis, a human gut microbe that can metabolize γBB into TMA, is sufficient to complete the carnitine→γBB→TMA transformation, elevate TMAO levels, and enhance thrombosis potential in recipients following arterial injury. RNAseq analyses of E. timonensis identified a 6 gene cluster, herein named gamma-butyrobetaine utilization gene cluster (gbu), which is upregulated in response to γBB. Combinatorial cloning and functional studies identified 4 genes (gbuA, gbuB, gbuC, and gbuE) that are necessary and sufficient to recapitulate the conversion of γBB to TMA when co-expressed in E. coli. Finally, reanalysis of samples (n=113) from a clinical randomized diet intervention study showed that the abundance of fecal gbuA correlates with plasma TMAO and a red meat-rich diet. Our findings reveal a microbial gene cluster that is critical to dietary carnitine→γBB→TMA→TMAO transformation in hosts and contributes to CVD risk.

Toward Personalized Oral Diagnosis: Distinct Microbiome Clusters in Periodontitis Biofilms.

Periodontitis is caused by pathogenic subgingival microbial biofilm development and dysbiotic interactions between host and hosted microbes. A thorough characterization of the subgingival biofilms by deep amplicon sequencing of 121 individual periodontitis pockets of nine patients and whole metagenomic analysis of the saliva microbial community of the same subjects were carried out. Two biofilm sampling methods yielded similar microbial compositions. Taxonomic mapping of all biofilms revealed three distinct microbial clusters. Two clinical diagnostic parameters, probing pocket depth (PPD) and clinical attachment level (CAL), correlated with the cluster mapping. The dysbiotic microbiomes were less diverse than the apparently healthy ones of the same subjects. The most abundant periodontal pathogens were also present in the saliva, although in different representations. The single abundant species Tannerella forsythia was found in the diseased pockets in about 16–17-fold in excess relative to the clinically healthy sulcus, making it suitable as an indicator of periodontitis biofilms. The discrete microbial communities indicate strong selection by the host immune system and allow the design of targeted antibiotic treatment selective against the main periodontal pathogen(s) in the individual patients.

Responses of bacterial taxonomic attributes to mercury species in rhizosphere paddy soil under natural sulphur-rich biochar amendment

Biochar and sulphur (S) are important factors regulating the level, speciation and transformation of mercury (Hg), leading to alterations in the assemblage of the soil microbial community. However, variations in the taxonomic attributes of the rhizosphere soil bacterial community arising from the Hg speciation in paddy soil, amended with natural S-rich biochar (NSBC) derived from the pyrolysis of S-rich oilseed rape straw, remain unclear. Herein, a rice pot experiment was conducted. Hg-polluted paddy soils were amended with NSBC and low-S biochar (LSBC) to evaluate the role of Hg chemical form affected by NSBC in regulating the taxonomic attributes of rhizosphere soil, including microbial abundance, composition, and ecological clusters within the co-occurrence network of microbial communities. Results showed that microbial abundance was higher in soils with lower Hg levels, and mean increases of 149 observed operational taxonomic units (OTUs) and 238 predicted OTUs (Chao 1) were observed, with a 1 mg kg−1 decrease in the total Hg (T-Hg) content. Among the 13 predictor variables, the T-Hg content was the strongest and most consistent predictor of the bacterial taxonomic attributes. This finding may be attributed to the fact that the drastic reduction in T-Hg and Hg bioavailability induced by NSBC results in the decrease of Hg stress on the soil microbiome. Moreover, NSBC amendment shifted the ecological clusters toward the amelioration of Hg pollution.

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.

Taxonomic structure and function of the corn stover degradative microbial consortium GF‐20 following growth on different sources of nitrogen

AbstractMicrobial consortia have substantial promise to degrade returned straw biomass and implement conversion strategies for soil nutrients to improve the quality of cultivated land. However, the composition of microbial consortia under different nitrogen conditions, the interaction between members and the functions during the process of decomposition of lignocellulose remain poorly understood. This study comprehensively examines the functional potential and structural diversity of the GF‐20 microbial consortium that degrades lignocellulose and soil used for inoculation and will explore the associated metabolic pathway networks in Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) using metagenomic analyses. Analyses of the metagenomic taxonomic affiliation data showed that the soil used for inoculation primarily contained members from the phyla Proteobacteria, Bacteroidetes, Acidobacteria, Chloroflexi and Acidobacteria, as well as Proteobacteria and Bacteroidetes in microbial consortia (N1 and N6). However, N6 is likely to be able to reduce the diversity of microbial species and change the community structure in a more concentrated comparison with N1. Notably, the key microbes were determined to be Cellvibrio, Brevundimonas, Flavobacterium and Achromobacter, whose analogous physiological functions were critical for the degradation of lignocellulosic substrates. The COG annotation indicated that the microbial metabolic cluster was the predominant category in all the samples, while the metabolic genes in N6 were relatively less abundant compared with those in N1. The KEGG annotation demonstrated that the inoculation soil (Q) has more metabolic functions and pathways than those of the microbial consortia, and the number of orthologies, modules, pathways and enzymes in N6 was observably lower than that in N1. A more detailed analysis showed that both of the consortia had functional profiles that were highly similar. These functional profiles clearly differed compared with those in the Q community. The relative abundance (RA) of ABC transporters in the Q was higher than that in the microbial consortia and higher in N1 than in N6. However, the two‐component system of N1 and N6 was higher than that of Q because of their relation to the microbial degradation of lignocellulosic materials. Most of the abundances of lignocellulolytic enzymes in the Q were lower than those in the microbial consortia (N1 and N6), and the RAs of some of these enzymes (e.g., β‐glucosidase, xylan 1,4‐β‐xylosidase, arabinoxylan arabinofuranohydrolase, β‐galactosidase, feruloyl esterase, mannan endo‐1,4‐β‐mannosidase, alpha‐glucuronidase and arabinogalactan endo‐1,4‐β‐galactosidase) in N6 were significantly higher than those of N1.The taxonomic structure and function of the Q and that of the consortia differed significantly, and the use of urea resulted in a decrease in the taxonomic species of microorganisms. The changes in functional diversity were accompanied with variation in the microbial composition, many of which were related to the microbial degradation of lignocellulolytic materials. Most of the degradative lignocellulolytic function in Q was lower than those of the microbial consortia N1 and N6, which aid in the degradation of straw.

Time-course alterations of gut microbiota and short-chain fatty acids after short-term lincomycin exposure in young swine.

Increasing evidence suggests that antibiotic administration causes gut injury, negatively affecting nutrient digestion, immune regulation, and colonization resistance against pathogens due to the disruption of gut microbiota. However, the time-course effects of therapeutic antibiotics on alterations of gut microbes and short-chain fatty acids (SCFAs) in young swine are still unknown. In this study, twenty piglets were assigned into two groups and fed commercial diets with or without lincomycin in the first week for a 28-day trial period. Results showed that 1-week lincomycin exposure (LE) did reduce the body weight on day 14 (p = 0.0450) and 28 (p = 0.0362). The alpha-diversity notably reduced after 1-week LE, and then gradually raised and reached the control group level in the second week on cessation of LE, indicated by the variation of Sobs, Chao, Shannon, and ACE index (p < 0.05). Beta-diversity analysis revealed that the distinct microbial cluster existed persistently for the whole trial period between two groups (p < 0.001). The relative abundance of most microbes including fiber-degrading (e.g., Agathobacter and Coprococcus), beneficial (e.g., Lactobacillus and Mitsuokella), or pathogenic bacteria (e.g., Terrisporobacter and Lachnoclostridium) decreased (LDA score > 3), and the concentration of SCFAs also diminished in the feces of 1-week lincomycin-administrated young swine, indicating that therapeutic LE killed most bacteria and reduced SCFA production with gut dysbiosis occurring. After the LE stopped, the state of gut dysbiosis gradually attenuated and formed new gut-microbe homeostasis distinct from microbial homeostasis of young pigs unexposed to lincomycin. The increased presence of potential pathogens, such as Terrisporobacter, Negativibacillus, and Escherichia-Shigella, and decreased beneficial bacteria, such as Lactobacillus and Agathobacter, were observed in new homeostasis reshaped by short-lincomycin administration (LDA score > 3 or p < 0.05), adversely affecting gut development and health of young pigs. Collectively, these results suggested that severe disruption of the commensal microbiota occurred after short-term LE or termination of LE in young swine. KEY POINTS: • Therapeutic lincomycin exposure induced gut dysbiosis, killing most bacteria and reducing short-chain fatty acid production. • Gut dysbiosis gradually attenuated and formed new homeostasis after lincomycin exposure stopped. • The new homeostasis, increased Escherichia-Shigella etc. and decreased Lactobacillus etc., was potentially harmful to gut health.

Ironing out the distribution of [2Fe-2S] motifs in ferrochelatases

Heme, a near ubiquitous cofactor, is synthesized by most organisms. The essential step of insertion of iron into the porphyrin macrocycle is mediated by the enzyme ferrochelatase. Several ferrochelatases have been characterized, and it has been experimentally shown that a fraction of them contain [2Fe-2S] clusters. It has been suggested that all metazoan ferrochelatases have such clusters, but among bacteria, these clusters have been most commonly identified in Actinobacteria and a few other bacteria. Despite this, the function of the [2Fe-2S] cluster remains undefined. With the large number of sequenced genomes currently available, we comprehensively assessed the distribution of putative [2Fe-2S] clusters throughout the ferrochelatase protein family. We discovered that while rare within the bacterial ferrochelatase family, this cluster is prevalent in a subset of phyla. Of note is that genomic data show that the cluster is not common in Actinobacteria, as is currently thought based on the small number of actinobacterial ferrochelatases experimentally examined. With available physiological data for each genome included, we identified a correlation between the presence of the microbial cluster and aerobic metabolism. Additionally, our analysis suggests that Firmicute ferrochelatases are the most ancient and evolutionarily preceded the Alphaproteobacterial precursor to eukaryotic mitochondria. These findings shed light on distribution and evolution of the [2Fe-2S] cluster in ferrochelatases and will aid in determining the function of the cluster in heme synthesis.

Exploring human-genome gut-microbiome interaction in Parkinson\u2019s disease

The causes of complex diseases remain an enigma despite decades of epidemiologic research on environmental risks and genome-wide studies that have uncovered tens or hundreds of susceptibility loci for each disease. We hypothesize that the microbiome is the missing link. Genetic studies have shown that overexpression of alpha-synuclein, a key pathological protein in Parkinson’s disease (PD), can cause familial PD and variants at alpha-synuclein locus confer risk of idiopathic PD. Recently, dysbiosis of gut microbiome in PD was identified: altered abundances of three microbial clusters were found, one of which was composed of opportunistic pathogens. Using two large datasets, we found evidence that the overabundance of opportunistic pathogens in PD gut is influenced by the host genotype at the alpha-synuclein locus, and that the variants responsible modulate alpha-synuclein expression. Results put forth testable hypotheses on the role of gut microbiome in the pathogenesis of PD, the incomplete penetrance of PD susceptibility genes, and potential triggers of pathology in the gut.

Biofilm prevalence and microbial characterisation in chronic wounds in a Sri Lankan cohort.

Biofilms have been associated with chronic wound infections in diabetic patients. The study assessed the occurrence of biofilms in chronic diabetic wounds (CDWs) in a Sri Lankan cohort. Tissue specimens collected during surgical debridement were analysed by quantitative differential viable counting, scanning electron microscopy (SEM), fluorescence insitu hybridization (FISH) and light microscopy with Gram and Haematoxylin-Eosin staining. All specimens harboured >5·0 log10 CFU per g bacteria and 2-9 distinct species per specimen were recovered from twenty wounds by culture. The most frequently isolated bacterium was Pseudomonas spp. (12/20;60%). Strict anaerobes were isolated from 10/20 specimens. Gram and Haematoxylin-Eosin staining showed aggregated micro-colonies, embedded in the wound tissue bed (20/20) but the exopolymer matrix was not visible in all samples (13/20). Fluorescence microscopy using a eubacteria-specific FISH probe indicated the presence of bacterial aggregates within the deep layers of the wound tissues (20/20). SEM revealed the presumptive architecture of matrix-embedded microbial clusters (20/20). The approximate diameter of bacterial aggregates in tissues ranged between 12 and 400µm. Bacterial infiltration into the internal portions of the tissues was apparent using FISH, Gram, and Haematoxylin-Eosin staining. All CDWs carried biofilm-specific morphological features. FISH was more specific than SEM and indicated the presence of microcolonies within deeper tissues.

Insights into rumen microbial biosynthetic gene cluster diversity through genome-resolved metagenomics

Ruminants are critical to global food security as they transform lignocellulosic biomass into high-quality protein products. The rumen microbes ferment feed to provide necessary energy and nutrients for the ruminant host. However, we still lack insight into the metabolic processes encoded by most rumen microbial populations. In this study, we implemented metagenomic binning approaches to recover 2,809 microbial genomes from cattle, sheep, moose, deer, and bison. By clustering genomes based on average nucleotide identity, we demonstrate approximately one-third of the metagenome-assembled genomes (MAGs) to represent species not present in current reference databases and rumen microbial genome collections. Combining these MAGs with other rumen genomic datasets permitted a phylogenomic characterization of the biosynthetic gene clusters (BGCs) from 8,160 rumen microbial genomes, including the identification of 195 lanthipeptides and 5,346 diverse gene clusters for nonribosomal peptide biosynthesis. A subset of Prevotella and Selenomonas BGCs had higher expression in steers with lower feed efficiency. Moreover, the microdiversity of BGCs was fairly constant across types of BGCs and cattle breeds. The reconstructed genomes expand the genomic representation of rumen microbial lineages, improve the annotation of multi-omics data, and link microbial populations to the production of secondary metabolites that may constitute a source of natural products for manipulating rumen fermentation.

Impact of systemic probiotics as adjuncts to subgingival instrumentation on the oral‐gut microbiota associated with periodontitis: A randomized controlled clinical trial

The oral-gut axis may be a route linking periodontal and systemic diseases. Probiotics could be an alternative for the treatment of microbial dysbiotic conditions, including periodontitis. This randomized placebo-controlled clinical trial evaluated the short-term efficacy of systemic probiotics adjunctive to subgingival instrumentation (SI) in promoting a better restoration of the oral-gut microbiotas and greater periodontal clinical outcome. Systemically healthy adults with untreated periodontitis were recruited from a Dental School setting and allocated to receive SI plus placebo (n=24) or probiotics (n=24), one capsule/day for 30 days. Subgingival biofilm and stool were obtained at baseline and 2-months post-therapy for microbiological analyses by checkerboard and 16S rRNA gene sequencing. Differences in all parameters between placebo (n=23) and probiotics (n=19) groups were assessed by non-parametric tests. Most subgingival species and α-diversity decreased after therapies (P<0.05), whereas gut composition/diversity were slightly or not affected by treatments. In parallel, significant clinical improvement (P<0.05) was similar between groups, although a trend for a higher proportion of poor responders in the placebo (60.8%) than the probiotic group (31.5%) was observed (P=0.07). Strong correlations between oral and fecal species were found (P<0.01), and distinct species related to poor response for different therapies (P<0.05). Patients were classified into five periodontitis oral-gut microbial clusters, which correlated differently with attachment loss after therapies (P<0.05). Systemic probiotics combined with SI did not provide short-term additional clinical or microbiological benefits in the treatment of periodontitis; however, response to therapies seemed to correlate with distinct oral-gut microbial profiles.

Exposure to High Aerial Ammonia Causes Hindgut Dysbiotic Microbiota and Alterations of Microbiota-Derived Metabolites in Growing Pigs.

Ammonia, an atmospheric pollutant in the air, jeopardizes immune function, and perturbs metabolism, especially lipid metabolism, in human and animals. The roles of intestinal microbiota and its metabolites in maintaining or regulating immune function and metabolism are irreplaceable. Therefore, this study aimed to investigate how aerial ammonia exposure influences hindgut microbiota and its metabolites in a pig model. Twelve growing pigs were treated with or without aerial ammonia (35 mg/m3) for 25 days, and then microbial diversity and microbiota-derived metabolites were measured. The results demonstrated a decreasing trend in leptin (p = 0.0898) and reduced high-density lipoprotein cholesterol (HDL-C, p = 0.0006) in serum after ammonia exposure. Besides, an upward trend in hyocholic acid (HCA), lithocholic acid (LCA), hyodeoxycholic acid (HDCA) (p < 0.1); a downward trend in tauro-deoxycholic acid (TDCA, p < 0.1); and a reduced tauro-HDCA (THDCA, p < 0.05) level were found in the serum bile acid (BA) profiles after ammonia exposure. Ammonia exposure notably raised microbial alpha-diversity with higher Sobs, Shannon, or ACE index in the cecum or colon and the Chao index in the cecum (p < 0.05) and clearly exhibited a distinct microbial cluster in hindgut indicated by principal coordinate analysis (p < 0.01), indicating that ammonia exposure induced alterations of microbial community structure and composition in the hindgut. Further analysis displayed that ammonia exposure increased the number of potentially harmful bacteria, such as Negativibacillus, Alloprevotella, or Lachnospira, and decreased the number of beneficial bacteria, such as Akkermansia or Clostridium_sensu_stricto_1, in the hindgut (FDR < 0.05). Analysis of microbiota-derived metabolites in the hindgut showed that ammonia exposure increased acetate and decreased isobutyrate or isovalerate in the cecum or colon, respectively (p < 0.05). Unlike the alteration of serum BA profiles, cecal BA data showed that high ammonia exposure had a downward trend in cholic acid (CA), HCA, and LCA (p < 0.1); a downward trend in deoxycholic acid (DCA) and HDCA (p < 0.05); and an upward trend in glycol-chenodeoxycholic acid (GCDCA, p < 0.05). Mantel test and correlation analysis revealed associations between microbiota-derived metabolites and ammonia exposure-responsive cecal bacteria. Collectively, the findings illustrated that high ammonia exposure induced the dysbiotic microbiota in the hindgut, thereby affecting the production of microbiota-derived short-chain fatty acids and BAs, which play a pivotal role in the modulation of host systematic metabolism.

OP29 Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome

Abstract Background The gut microbiome directly affects the balance of pro-inflammatory and anti-inflammatory responses in the gut. As microbes thrive on dietary substrates, the question arises whether we can nourish an anti-inflammatory gut ecosystem. In this study, we investigated the relation between 173 dietary factors and the microbiome of 1425 individuals spanning four cohorts: Crohn’s disease, ulcerative colitis, irritable bowel syndrome and the general population. Methods Shotgun metagenomic sequencing was performed to profile gut microbial composition and function. Dietary intake was assessed through food frequency questionnaires. We performed unsupervised clustering to identify dietary patterns and microbial clusters. Next, linear models were conducted between dietary intake and microbial species and pathways, adding age, sex, caloric intake and sequencing read depth as covariates. Analyses were conducted per cohort, followed by a meta-analysis and heterogeneity estimation. Multiple testing correction was performed on the obtained p-values and a FDR &amp;lt;0.05 was defined as significance cut-off. Results We identified 38 associations between dietary patterns and microbial clusters. Moreover, 61 individual foods and nutrients were associated with 61 species and 249 metabolic pathways in the meta-analysis across healthy individuals and patients with IBS, Crohn’s disease and UC (FDR&amp;lt;0.05, heterogeneity p-value&amp;gt;0.05). Processed foods and animal-derived foods were consistently associated with higher abundances of Firmicutes, Ruminococcus species of the Blautia genus and endotoxin synthesis pathways. The opposite associations were found for clusters comprising fish, nuts, bread and legumes. Moreover, while total plant protein intake was associated with a higher Bifidobacterium abundance (FDR=0.048, coef=4.98), animal-derived protein showed a negative association (FDR=1.30x10-05, coef= -4.1). Lastly, we observed positive associations of fecal calprotectin with a fast food cluster (FDR=4.14x10-4, coef=0.24) and a cluster comprised of high-fat meat, potatoes and gravy (FDR=0.003, coef =0.22), while the opposite was seen for clusters of fish and nuts (FDR=0.038, coef= -0.1) and bread and legumes (FDR=0.005, coef= -2.48). Conclusion We identified dietary patterns that consistently correlate with groups of bacteria with shared functional roles in both, health and disease. Moreover, specific foods and nutrients were associated with species known to infer mucosal protection and anti-inflammatory effects. A decrease in these bacteria has already been associated with both IBS and IBD. We propose microbial mechanisms through which the diet affects inflammatory responses in the gut as a rationale for future intervention studies.