Characterization Of Microbiome Research Articles

Differences in maternal subgingival microbiome between preterm and term births: The MOHEPI study.

Periodontitis is a potential risk factor for preterm birth (PTB) in women; however, the causal relationship or the exact mechanism remain unknown. This study aimed to compare the oral microbiome features of mothers with full-term birth (FTB) with those who had preterm delivery. This study prospectively enrolled 60 women (30 mothers with PTB and 30 mothers with FTB), and subgingival plaque samples were collected and analysed by metagenomic 16S rDNA sequencing. Clinical measurements, including periodontal probing depth, clinical attachment level, modified gingival index (mGI) and plaque index, were performed to determine the periodontal state of the participants. Medical and obstetric data were collected as well. Among the periodontal measurements, mGI score, reflecting the level of gingival inflammation, exhibited a statistically significant association with PTB (adjusted odds ratio 2.705, 95% confidence interval 1.074-6.811, p = .035). When subgroup analysis was conducted based on mean mGI scores (mGI ≥ 2, high inflammation [HI] versus mGI < 2, low inflammation [LI]), microbiome analysis revealed clear distinctions in microbial compositions between PTB and FTB mothers in both the HI and LI groups. Especially in the HI group, alpha diversity exhibited a decreasing trend in PTB mothers compared to FTB mothers. Beta diversity also revealed significant differences between the two groups. In Linear Discriminant Analysis Effect Size analysis, certain anaerobic taxa, including the genera Spirochaetes, Treponema and Porphyromonas, were relatively abundant in the FTB/HI group, whereas the PTB/HI group showed a high abundance of the order Actinomycetales. Network analysis showed that the FTB/HI had relatively stronger connectivity in microbial composition than the PTB/HI group. Dysbiosis ratio of plaque microbiome, in terms of periodontitis, was significantly lower in PTB/HI group compared to FTB/HI group. The compositions of maternal subgingival microbiomes differed between PTB and FTB mothers in both the high and low levels of gingival inflammation groups. In the presence of high level of gingival inflammation, dysbiosis in plaque microbiome, in terms of periodontitis, was decreased in PTB mothers compared to FTB mothers.

An Eastern County from an European Eastern Country—The Characteristics of Cutaneous Microbiome in Psoriasis Patients—Preliminary Results

The cutaneous microbiome represents a topic of high interest nowadays. Multiple studies have suggested the importance of the skin microbiome in different dermatological pathologies, highlighting the possible implications of cutaneous microorganisms in either the pathogenesis or prognosis of skin maladies. Psoriasis represents a common inflammatory skin disease, with a high prevalence in the worldwide population. The role of the cutaneous microbiome in psoriasis could explain a number of pathogenic theories and treatment objectives of this incurable skin disease. Our interest in the characteristics of the cutaneous microbiome, especially in psoriatic patients who attended a tertiary dermatological centre in Galati, Romania, is reflected in our current study, of which the preliminary results are discussed in this article. Using three types of skin sampling techniques (swabs, adhesive tape, and punch biopsies), we tried to characterise the microorganisms harboured in the skin of psoriatic patients and healthy individuals. This study was performed using culture-based probes, which were analysed using MALDI-TOF mass spectrometer equipment. Our preliminary results suggested that the greatest diversity was observed in the perilesional areas of psoriatic patients. The lowest cutaneous diversity was obtained from sampling psoriatic plaques. These results are similar to other studies of the cutaneous microbiome in psoriasis. The most frequent microorganisms found in all groups studied were of the Staphylococcus species: Staphylococcus epidermidis, Staphylococcus hominis, and Staphylococcus aureus. Analysing the living environment of each individual from this study, our preliminary results suggested different results from other studies, as higher diversity and heterogenicity was observed in urban environments than in rural living areas. Regarding the differences between sexes, our preliminary results showed higher quantitative and qualitative changes in the skin microbiome of male participants than female participants, opposite to the results found in other studies of the cutaneous microbiome in psoriasis. Given these preliminary results, we can conclude that we have found important differences by studying the cutaneous microbiome of psoriatic patients and healthy control individuals from a population that, to our knowledge, has not been yet studied from this point of view. Our results showed important characteristics of the skin microbiome in an Eastern European population, where cultural and environmental living habits could influence the cutaneous microbiome.

Proof of Concept Study: Comparability of Microbiome Diversity in Self- and Physician-Collected HPV-Positive and HPV-Negative Cervicovaginal Samples

Recent studies have revealed the impact of human papillomavirus (HPV) infections on the cervicovaginal microbiome; however, few have explored the utility of self-collected specimens (SCS) for microbiome detection, obtained using standardised methods for HPV testing. Here, we present a proof-of-concept analysis utilising Oxford Nanopore sequencing of the 16S rRNA gene in paired samples collected either by the patient using an Evalyn Brush or collected by a physician using liquid-based cytology (LBC). We found no significant differences in the α-diversity estimates between the SCS and LBC samples. Similarly, when analysing β-diversity, we observed a close grouping of paired samples, indicating that both collection methods detected the same microbiome features. The identification of genera and Lactobacillus species in each sample allowed for their classification into community state types (CSTs). Notably, paired samples had the same CST, while HPV-positive and -negative samples belonged to distinct CSTs. As previously described in other studies, HPV-positive samples exhibited heightened bacterial diversity, reduced Lactobacillus abundance, and an increase in genera like Sneathia or Dialister. Altogether, this study showed comparable results between the SCS and LBC samples, underscoring the potential of self-sampling for analysing the microbiome composition in cervicovaginal samples initially collected for HPV testing in the context of cervical cancer screening.

Microbiome dynamics during malting of barley grains infested by Fusarium graminearum strains

AbstractBarley grain harvested for malting poses an interesting case study for the impacts of plant‐associated microbiomes because the conditions created during malting favour continued vigorous microbial activity after grain harvest. Suppression of pathogens is among the key functions performed by microbiomes, and it would be beneficial if we could harness this function. Over a 3‐year field trial, we micro‐malted barley that had been experimentally infested with each of seven different strains of the fungal pathogen Fusarium graminearum, and profiled bacterial microbiomes at key stages in the malting process (grain, post‐steeping, post‐germination and final dried malt). The greatest impacts on bacterial microbiomes were observed to be from the year and stage of malting, with comparatively fewer impacts of barley cultivar or pathogen strain. Relatively limited impacts of the presence and strain identity of fungal pathogen on the bacterial microbiome of malting barley probably reflects the colonization by other fungi, as our inoculation took place under field conditions with supplemental irrigation. Both community level shifts and significant responses by individual taxa were evident. Microbiome characteristics or the relative abundances of specific bacterial taxa helped to explain pathogen biomass, mycotoxin production and beer gushing. Manipulative experiments will be required to test hypotheses suggested by these microbiome profiles.

#2227 Exploring the interplay between gut microbiome, fecal metabolomics and ambulatory blood pressure in white-coat hypertensive patients

Abstract Background and Aims Recent evidence showed the relationship between gut microbiota with hypertension. Few studies also demonstrated that ambulatory blood pressure monitoring variables such as dipping status and linear variability are associated with fecal microbiota and metabolomics. However, the relationship between gut microbiota and metabolomic composition of white-coat hypertensive patients has not been studied yet. In addition, although the link between gut microbiota, blood pressure variability and high salt intake has been shown, none of the studies addressed these changes simultaneously in the same study population. Here, we aimed to investigate the interplay between the gut microbiome, fecal metabolites and 24-hour urine sodium levels between hypertensive, white-coat hypertensive (WCH) and healthy participants diagnosed with ambulatory blood pressure monitoring. Method The study included 18 newly diagnosed hypertensive, 8 WCH, and 21 healthy participants from our tertiary center. Ambulatory blood pressure (BP) monitoring was performed in all participants and nighttime dipping, morning BP surge (MBPS), pre-wake MBPS and linear BP variability were calculated. 16S rRNA sequencing was performed using Illumina MiSeq sequencer. DeSeq2 and linear discriminant analysis effect size (LEfSe) were performed with R. Fecal metabolite levels were analyzed by GC-MS. A partial least squares-discriminant analysis (PLS-DA) model was constructed for the feature selector and classifier. The variable importance in the projection (VIP) coefficient was calculated based on the PLS-DA model. Results ANOVA and post-hoc Tukey test showed WHC and hypertensive groups had higher blood pressure variability and morning-thorough MBPS than normotensive patients (p = 0.02 and 0.04, respectively), whereas 24-h urine Na levels were statistically similar between WCH and hypertensive groups (p = 0.11). There were no significant differences in α- and β-diversity metrics of gut microbiome between study groups. Select taxa were specific to WHC patients, notably Rikenellaceae family and Mitsuokella were higher in WHC against normotensive patients, whereas Ruminococcus callidus, Roseburia, Clostridium, Lactobacillus ruminis, Sutterall, Lachospiraceae and Muribaculaceae were decreased in WHC against normotensive patients in DeSeq2 analysis. Dialister was increased, whereas Bacteroides genus and Bacteroides fragilis were decreased in WHC against hypertensive patients. LEfSe analysis showed positive enrichment in Proteobacteria phylum and negative enrichment in Mitsuokella genus in WHC against hypertensive group. Enterococcus, Lachnobacterium, Odoribacter and Pseudomonas genera had positive; whereas Lactobacillus and Clostridium had negative correlations with 24-h urine Na levels. Positive correlations were shown between linear BP variability and Bacteroides and Paraprevotella genera. Several genera and species were enriched in Q3-4 against Q1-2 quartiles of pre-wake and sleep-thorough MBPS in LEfSe analyzes (Fig. 1). Normotensive and essential hypertensive groups could also be differentiated based on fecal metabolomic composition. Specifically, metabolites with the highest VIP values discriminating WCH from normotensive and hypertensive groups were methyl-palmitoleate, oxalic acid and phenyl β-D-glucopyranoside, respectively (Fig. 2). Conclusion In conclusion, we performed the first study focusing on the fecal microbiome and metabolomic characteristics of white-coat hypertensive patients. Urine Na levels and ambulatory blood pressure variables of the WCH group are different than those of the normotensive and similar to the hypertensive group. Comparative and correlation analyses revealed novel relationships between ambulatory blood pressure variables and gut microbiome of both WCH and hypertensive patients. Fecal metabolomic differences between study groups imply possible mechanisms underlying the effects of gut microbiome on blood pressure. Gut microbiota and metabolites may become valuable targets for interventions of both white-coat and essential hypertension in the near future.

Leveraging existing 16S rRNA gene surveys to decipher microbial signatures and dysbiosis in cervical carcinogenesis

The presence of dysbiotic cervicovaginal microbiota has been observed to be linked to the persistent development of cervical carcinogenesis mediated by the human papillomavirus (HPV). Nevertheless, the characteristics of the cervical microbiome in individuals diagnosed with cervical cancer (CC) are still not well understood. Comprehensive analysis was conducted by re-analyzing the cervical 16S rRNA sequencing datasets of a total of 507 samples from six previously published studies. We observed significant alpha and beta diversity differences in between CC, cervical intraepithelial neoplasia (CIN) and normal controls (NC), but not between HPV and NC in the combined dataset. Meta-analysis revealed that opportunistic pernicious microbes Streptococcus, Fusobacterium, Pseudomonas and Anaerococcus were enriched in CC, while Lactobacillus was depleted compared to NC. Members of Gardnerella, Sneathia, Pseudomonas, and Fannyhessea have significantly increased relative abundance compared to other bacteria in the CIN group. Five newly identified bacterial genera were found to differentiate CC from NC, with an area under the curve (AUC) of 0.8947. Moreover, co-occurrence network analysis showed that the most commonly encountered Lactobacillus was strongly negatively correlated with Prevotella. Overall, our study identified a set of potential biomarkers for CC from samples across different geographic regions. Our meta-analysis provided significant insights into the characteristics of dysbiotic cervicovaginal microbiota undergoing CC, which may lead to the development of noninvasive CC diagnostic tools and therapeutic interventions.

Comparative microbiome analysis in cystic fibrosis and non-cystic fibrosis bronchiectasis.

Bronchiectasis is a condition characterized by abnormal and irreversible bronchial dilation resulting from lung tissue damage and can be categorized into two main groups: cystic fibrosis (CF) and non-CF bronchiectasis (NCFB). Both diseases are marked by recurrent infections, inflammatory exacerbations, and lung damage. Given that infections are the primary drivers of disease progression, characterization of the respiratory microbiome can shed light on compositional alterations and susceptibility to antimicrobial drugs in these cases compared to healthy individuals. To assess the microbiota in the two studied diseases, 35 subjects were recruited, comprising 10 NCFB and 13 CF patients and 12 healthy individuals. Nasopharyngeal swabs and induced sputum were collected, and total DNA was extracted. The DNA was then sequenced by the shotgun method and evaluated using the SqueezeMeta pipeline and R. We observed reduced species diversity in both disease cohorts, along with distinct microbial compositions and profiles of antimicrobial resistance genes, compared to healthy individuals. The nasopharynx exhibited a consistent microbiota composition across all cohorts. Enrichment of members of theBurkholderiaceaefamily and an increased Firmicutes/Bacteroidetes ratio in the CF cohort emerged as key distinguishing factors compared to NCFB group.Staphylococcus aureusand Prevotella shahii also presented differential abundance in the CF and NCFB cohorts, respectively, in the lower respiratory tract. Considering antimicrobial resistance, a high number of genes related to antibiotic efflux were detected in both disease groups, which correlated with the patient's clinical data. Bronchiectasis is associated with reduced microbial diversity and a shift in microbial and resistome composition compared to healthy subjects. Despite some similarities, CF and NCFB present significant differences in microbiome composition and antimicrobial resistance profiles, suggesting the need for customized management strategies for each disease.

P29 Long-read sequencing provides unprecedented insight into the skin and wound microbial landscape

Abstract Introduction and aims It is becoming increasingly evident that the microbial inhabitants of our skin play a key role in cutaneous health and disease. However, our understanding of the contribution of the complex skin microbiome to wound healing outcome remains incomplete. This is, in part, due to the historic challenges around traditional sampling and profiling Methods, which often fail to capture the abundance and diversity of the skin microbiome. Recent advances in microbiome sequencing technologies now enable more comprehensive characterization of skin bacterial composition and host-microbe interactions. Thus, the aim of this study was to utilize a novel long-read sequencing platform to provide species-level microbiome characterization and deliver important insight into the drivers of pathological skin repair. Methods Microbial DNA samples were collected from the skin and wounds of healthy volunteers and patients with chronic wounds (n = 40 per group). Long-read nanopore sequencing was used to profile microbiome samples, while RNA-Seq enabled generation of donor transcriptomic profiles. A multifaceted approach was used to integrate these datasets to investigate the complex interplay between host skin pathology and the microbiome. Results We first identified perturbations in the skin microbiome of patients with chronic wounds, which was significantly less diverse than healthy skin and colonized with key bacteria associated with pathogenicity. These alterations in the skin microbiome also correlated with transcriptomic changes, such as upregulation of genes associated with inflammation, stress and poor healing. Interestingly, long-read sequencing data displayed poor correlation with routine clinical microbiology swabs, while specific clinical characteristics (e.g. glycaemic control and wound duration) were strongly linked to wound microbiome composition. Conclusions Collectively, these data provide crucial new insight into the skin and wound microbial landscape, demonstrating a potential role for specific wound bacteria in modulating pathological skin repair.

Quantitative microbiome profiling of honey bee (Apis mellifera) guts is predictive of winter colony loss in northern Virginia (USA)

For the past 15 years, the proportion of honey bee hives that fail to survive winter has averaged ~ 30% in the United States. Winter hive loss has significant negative impacts on agriculture, the economy, and ecosystems. Compared to other factors, the role of honey bee gut microbial communities in driving winter hive loss has received little attention. We investigate the relationship between winter survival and honey bee gut microbiome composition of 168 honey bees from 23 hives, nine of which failed to survive through winter 2022. We found that there was a substantial difference in the abundance and community composition of honey bee gut microbiomes based on hive condition, i.e., winter survival or failure. The overall microbial abundance, as assessed using Quantitative Microbiome Profiling (QMP), was significantly greater in hives that survived winter 2022 than in those that failed, and the average overall abundance of each of ten bacterial genera was also greater in surviving hives. There were no significant differences in alpha diversity based on hive condition, but there was a highly significant difference in beta diversity. The bacterial genera Commensalibacter and Snodgrassella were positively associated with winter hive survival. Logistic regression and random forest machine learning models on pooled ASV counts for the genus data were highly predictive of winter outcome, although model performance decreased when samples from the location with no hive failures were excluded from analysis. As a whole, our results show that the abundance and community composition of honey bee gut microbiota is associated with winter hive loss, and can potentially be used as a diagnostic tool in evaluating hive health prior to the onset of winter. Future work on the functional characterization of the honey bee gut microbiome’s role in winter survival is warranted.

The microbiomic signature of hemorrhoids and comparison with associated microbiomes.

Hemorrhoids are a common ailment that can cause significant disruptions to one's daily life. While some researchers have speculated about a potential link between hemorrhoid development and gut microbes, there is currently insufficient evidence to support this claim. In this study, we collected samples from 60 hemorrhoid patients and analyzed the composition and characteristics of microbiomes in hemorrhoids. PCoA results revealed distinct differences between the microbiomes of hemorrhoids, skin-originated microbiomes, and gut microbes, highlighting the complex nature of hemorrhoidal microbiomes. The distribution characteristics of Staphylococcus suggest that the skin microbiome influences the microbiome of hemorrhoids. Additionally, we observed higher levels of Prevotella in two cases of thrombosed hemorrhoids compared to non-thrombosed hemorrhoids. This finding suggests that Prevotella may play a crucial role in the development of thrombosed hemorrhoids.

Comparative characterization of supragingival plaque microbiomes in malocclusion adult female patients undergoing orthodontic treatment with removable aligners or fixed appliances: a descriptive cross-sectional study.

This study aimed to explore the effects of removable aligners and fixed appliances on the supragingival bacterial communities in adult female patients undergoing orthodontic treatment. Supragingival plaque samples from 48 female individuals underwent microbiome analysis (16S rRNA gene sequencing) using PacBio Sequel sequencing. The study included 13 adults without orthodontic treatment needs as the control group (Group C), and 35 patients with comparable initial orthodontic conditions who received treatment at a university clinic in Beijing, China. The treatment involved either traditional fixed brackets (Group B, n = 17) or Invisalign® aligners (Group AT, n = 18). Bioinformatics methods were used for data analysis. From the 48 plaque samples, a total of 334,961 valid reads were obtained, averaging 6,978 sequences per sample. The 16S rDNA sequences were classified into 25,727 amplicon sequence variants (ASVs). Significant variances in alpha and beta diversity among the groups were noted. Group B microbiome exhibited an increased presence of Gram-negative bacteria. At the phylum level, Actinobacteriota was significantly more prevalent in Group C samples, while Bacteroidota was enriched in Group B samples. Family-level relative abundance analysis showed a notable increase in Saccharibacteria (formerly TM7) and Prevotellaceae in Group B. Genus-level analysis revealed a significant rise in Lautropia in Group AT. Fixed orthodontic appliances were linked to oral microbiome changes, notably an enhanced relative abundance of anaerobes, including periodontal pathogens. The observation points to the impact of orthodontic appliance on the oral microbial community, highlighting the difference between traditional braces (Group B) and clear aligners (Group AT)in terms of the predominance of anaerobic and gram negative bacteria. This emphasizes the importance of considering the microbiological effects when choosing orthodontic appliance and underscores the need for tailored oral hygiene practices for individuals undergoing these treatments. This research might provide insights that could assist in the development of innovative cleaning techniques and antibacterial materials.

Characterization and functional prediction of the dental plaque microbiome in patients with alveolar clefts.

Alveolar cleft (AC) is a common congenital defect in people with cleft lip and palate (CLP). Alveolar bone grafting (ABG) is typically performed during adolescence, resulting in the fissure remaining in the mouth for a longer length of time. Patients with AC have a greater rate of oral diseases such as dental caries than the normal population, and the precise characteristics of the bacterial alterations caused by AC are unknown. We recruited a total of 87 subjects and collected dental plaque samples from AC adolescents (AAP), post-operative ABG adolescents (PAP), healthy control adolescents (CAP), AC young adults (AYP), post-operative ABG young adults (PYP), and healthy control young adults (CYP). The sequencing of 16S rRNA genes was performed. The microbial composition of plaque from alveolar cleft patients differed significantly from age-matched healthy controls. Linear discriminant analysis effect size (LEfSe) analysis revealed that AAP was enriched for Neisseria, Haemophilus, Fusobacterium, Rhodococcus, Aggregatibacter, Gemella, and Porphyromonas, whereas AYP was enriched for Capnocytophaga, Rhodococcus, and Actinomyces-f0332. There were phenotypic differences in facultatively anaerobic, Gram-negative, Gram-positive, and oxidative stress tolerance between the AYP group with longer alveolar cleft and the healthy control group according to Bugbase phenotypic predictions. Alveolar bone grafting did not alter the functional phenotype of alveolar cleft patients but reduced the number of differential genera between alveolar cleft patients and healthy controls at both ages. Our study systematically characterized the supragingival plaque microbiota of alveolar cleft patients, post-alveolar bone grafting patients, and matched healthy controls in two ages to gain a better understanding of plaque ecology and microbiology associated with alveolar clefts.

Characterization of seminal microbiome associated with semen parameters using next-generation sequencing

BackgroundTo characterize the seminal microbiome associated with normal and abnormal semen parameters, towards the prediction of reproductive health and sperm quality. Despite the association between bacteria and infertility, few studies have looked at the beneficial effects of the seminal microbiome on infertility.The study comprised semen samples from 69 men with normal spermiograms and 166 men with at least 1 abnormal spermiogram parameter from the Institutional IVF Center between October 2019 and October 2022.We hypothesized that the composition of the microbiota may affect semen parameters. To determine the composition of uncultured bacteria, the 16S ribosomal RNA (rRNA) gene was amplified using Oxford Nanopore Technology.ResultsDifferent groups of bacteria were present in the semen samples of patients with normal semen parameters, such as female factor infertility and abnormal sperm parameters. Bacterial communities differed between samples. However, the relative distribution of Lactobacillus and Prevotella in the normal and abnormal semen groups differed (p = 0.05) and was statistically significant.In the abnormal semen group, the incidence of Lactobacillus probiotics was lower and the frequency of Prevotella was higher. Additionally, principal component analysis (PCA) revealed differences in the microbial composition of normal and abnormal semen.ConclusionsIn our study, NGS analysis revealed the increased presence of harmful bacteria Prevotella in groups with abnormal semen raises the possibility that certain microbiota may be associated with semen quality and male infertility.

Metagenomic dissection of the intestinal microbiome in the giant river prawn Macrobrachium rosenbergii infected with Decapod iridescent virus 1

Microbiome in the intestines of aquatic invertebrates plays pivotal roles in maintaining intestinal homeostasis, especially when the host is exposed to pathogen invasion. Decapod iridescent virus 1 (DIV1) is a devastating virus seriously affecting the productivity and success of crustacean aquaculture. In this study, a metagenomic analysis was conducted to investigate the genomic sequences, community structure and functional characteristics of the intestinal microbiome in the giant river prawn Macrobrachiumrosenbergii infected with DIV1. The results showed that DIV1 infection could significantly reduce the diversity and richness of intestinal microbiome. Proteobacteria represented the largest taxon at the phylum level, and at the species level, the abundance of Gonapodya prolifera and Solemya velum gill symbiont increased significantly following DIV1 infection. In the infected prawns, four metabolic pathways related to purine metabolism, pyrimidine metabolism, glycerophospholipid metabolism, and pentose phosphate pathway, and five pathways related to nucleotide excision repair, homologous recombination, mismatch repair, base excision repair, and DNA replication were significantly enriched. Moreover, several immune response related pathways, such as shigellosis, bacterial invasion of epithelial cells, Salmonella infection, and Vibrio cholerae infection were repressed, indicating that secondary infection in M. rosenbergii may be inhibited via the suppression of these immune related pathways. DIV1 infection led to the induction of microbial carbohydrate enzymes such as the glycoside hydrolases (GHs), and reduced the abundance and number of antibiotic-resistant ontologies (AROs). A variety of AROs were identified from the microbiota, and mdtF and lrfA appeared as the dominant genes in the detected AROs. In addition, antibiotic efflux, antibiotic inactivation, and antibiotic target alteration were the main antibiotic resistance mechanisms. Collectively, the data would enable a deeper understanding of the molecular response of intestinal microbiota to DIV1, and offer more insights into its roles in prawn resistance to DIVI infection.

192 Effects of inclusion of a probiotic and/or a postbiotic in diets containing a phytogenic feed additive on growth performance and fecal microbiome composition and function of nursery pigs

Abstract This study investigated the effects of inclusion of a Bacillus-based probiotic and a postbiotic from Lactobacillus acidophilus fermentation (Dia-V Nursery, Diamond V, IA) in diets containing a phytogenic feed additive (Fresta Protect, Delacon, Austria) on growth performance and fecal microbiome of pigs. Weaned pigs [n = 1,840; 19 d old; initial body weight (BW) = 6.1 ± 0.2 kg] were allotted to 16 replicate pens/ treatment (23 pigs/pen) in 2 barns. Pens were blocked by location within barn and randomly allotted to 5 treatments: 1) Basal diet (NC), 2) NC without specialty fats (soy oil blend and medium chain fatty acid blend) + 0.1% phytogenic (PC), 3) PC + 0.05% probiotic (1.1 x 106 CFU/kg of complete feed; PC+Prob), 4) PC + 0.2% postbiotic (PC+Post), and 5) PC + 0.05% probiotic + 0.2% postbiotic (PC+Prob+Post). Pigs were fed experimental diets during phase 1 (d 0-10) and 2 (d 10-23). Pig and feed weights were recorded at the beginning and end of each phase. Fecal samples were collected from 2 pigs/pen (n = 32/treatment) on d 7 and 25 post-wean and subjected to DNA extraction and shotgun metagenomics to evaluate gut microbiome. Performance data were analyzed using the lme4 package of R with treatment as fixed effect and barn and pen location within barn as random effects. Microbiome data were center-log-ratio transformed and analyzed for alpha- and beta-diversity, differentially abundant taxa and genes, microbial network, and carbohydrate active enzymes (CAZy). No differences on performance, mortality or removals were observed during phase 1, phase 2, or overall among treatments (Table 1). Microbiome features were similar between NC and PC. The PC+Prob did not affect alpha- and beta-diversities of microbiome. The PC+Post reduced (P &amp;lt; 0.05) alpha-diversity on d 7 compared with PC and affected (P &amp;lt; 0.05) beta-diversity on both timepoints. The PC+Post had the greatest number of differentially abundant taxa (P &amp;lt; 0.05) compared with PC both on d 7 (27 taxa) and 25 (14 taxa). The PC+Post had greater (P &amp;lt; 0.05) presence of CAZy including glycoside hydrolases, glycosyltransferases and carbohydrate-binding modules on both timepoints. Inclusion of probiotic and postbiotic separately or in combination reduced (P &amp;lt; 0.05) the number of positive connections within the microbial network suggesting these additives promoted a more competitive microbial ecosystem against opportunistic microorganisms compared with PC. Inclusion of postbiotic speeded up the progression of microbiome toward a more mature community. This resulted in reduction of diversity but increased carbohydrate enzyme capability making microbial community leaner and more effective. In conclusion, replacement of specialty fats with a phytogenic did not affect piglet performance or microbiome under non-challenge conditions and no differences in performance were observed between PC pigs and those supplemented with a probiotic or postbiotic despite the effects observed in microbiome.

226 Oral and rumen microbiome characterization to predict host phenotypes

Abstract Studies have utilized rumen microbiome composition and function to predict animal phenotypes. Yet, sample collection for rumen microbial community analysis can be difficult and invasive and hinders the possibility of sampling large animal populations. In this study, we investigated the development of the bovine rumen microbiome over time, to identify the potential of the oral microbiome as a proxy for the rumen microbiome, and to test the applicability of using the oral microbiome for predicting phenotypes in beef cattle. We employed 16S rRNA amplicon sequencing to characterize the rumen and oral bacterial community structure over time and collected both birth and weaning weights in a population of 220 animals. Our findings show that both the oral and rumen microbiomes are established early, and a significant portion of the taxa persists even after weaning. We identified a group of core successional species shared between the oral and rumen bacterial communities, which are established early and persist over time. The oral bacterial community was dominated by phyla Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteria, while the rumen bacterial community was dominated by phyla Bacteroidota, Firmicutes, Verrucomicrobia, Fibrobacteria, and Spirochaetota. Furthermore, we observed that 38% of Amplicon Sequence Variants (ASVs) were shared between the oral and rumen microbiomes at 50 to 120 d of age. At 170 to 240 d of age, 37% of ASVs were shared, and at 295 to 365 d, 33% of ASVs were shared. Finally, at 400 to 468 d, 21% of ASVs were shared. Based on weighted Unifrac analysis, notable differences and distinct clustering was observed between oral and rumen microbiome communities at different sampling ages (P = 0.001; R2 = 0.50969, 50 to 120; P = 0.001; R2 = 0.66247, 170 to 240; P = 0.001; R2 = 0.62036, 295 to 365; and P = 0.001, R2 = 0.66559, 400 to 468). Microbiability estimates varied across different stages and microbial environments. For the oral bacterial community at 50 to 120, the estimates were 0.029%, 0.032%, 0.029%, and 0.028% for birth weight, weaning weight, intramuscular fat (IMF), and ribeye area (REA), respectively. In contrast, the rumen microbiome exhibited microbiability values of 0.034%, 0.058, 0.059, and 0.069% for birth weight, weaning weight, IMF, and REA respectively during the same period. As the animal aged the microbiability increased. At 170 to 240, oral microbiomes showed microbiability estimates of 0.051%, 0.060%, 0.069%, and 0.21% for birth weight, weaning weight, IMF, and REA respectively. In comparison, the rumen microbiome displayed greater microbiability estimates of 0.12%, 0.124%, 0.20%, and 0.26% for birth weight, weaning weight, IMF, and REA respectively. In conclusion, the oral microbiome is not a good proxy for the rumen microbiome composition; however, there is potential to use the oral microbiome for phenotype prediction.

Gut microbiome and resistome characterization of pigs treated with commonly used post-weaning diarrhea treatments

BackgroundThe global burden of antimicrobial resistance demands additional measures to ensure the sustainable and conscious use of antimicrobials. For the swine industry, the post-weaning period is critical and for many years, antimicrobials have been the most effective strategy to control and treat post-weaning related infections. Among them, post-weaning diarrhea causes vast economic losses, as it severely compromises piglets’ health and growth performance. In this study, 210 piglets were transferred from a farm with recurrent cases of post-weaning diarrhea to an experimental farm and divided into six different treatment groups to determine the effect of the different treatments on the growth performance and survival, the microbiome, and the resistome in a cross-sectional and longitudinal study. The different treatments included antimicrobials trimethoprim/sulfamethoxazole, colistin, and gentamicin, an oral commercial vaccine, a control with water acidification, and an untreated control. An extra group remained at the farm of origin following the implemented amoxicillin routine treatment. A total of 280 fecal samples from pigs at four different sampling times were selected for metagenomics: before weaning-treatment at the farm of origin, and three days, two weeks, and four weeks post-treatment.ResultsThe control group with water acidification showed a reduced death risk in the survival analyses and non-significant differences in average daily weight gain in comparison to the antibiotic-treated groups. However, the growth-promoting effect among antibiotic-treated groups was demonstrated when comparing against the untreated control group at the experimental farm. After four weeks of treatment, diversity indexes revealed significantly decreased diversity for the untreated control and the group that remained at the farm of origin treated with amoxicillin. For this last group, impaired microbial diversity could be related to the continuous amoxicillin treatment carried out at the farm. Analysis of the resistome showed that both gentamicin and amoxicillin treatments significantly contributed to the emergence of resistance, while trimethoprim/sulphonamide and colistin did not, suggesting that different treatments contribute differently to the emergence of resistance.ConclusionsOverall, this shotgun longitudinal metagenomics analysis demonstrates that non-antibiotic alternatives, such as water acidification, can contribute to reducing the emergence of antimicrobial resistance without compromising pig growth performance and gut microbiome.

Abstract PO4-03-04: Characterization of Gut Microbiome of patients with early-stage breast cancer treated with neoadjuvant chemotherapy

Abstract Objective: The gut microbiome (GM) has been identified as one of the major environmental factors that can regulate the development and maintenance of the immune system. In oncology, while the importance of GM has been evaluated in more immunogenic tumors such as melanoma, lung carcinoma and clear cell carcinoma, its importance in early-stage breast cancer (eBC) is underexplored. The aim of this study was to characterize the GM of patients with eBC who underwent neoadjuvant chemotherapy (NACT) and to evaluate its association with clinicopathologic prognostic factors and outcomes. Methods: This was a prospective study conducted at two Brazilian institutions. Fecal samples were collected at baseline (time 1) and prior to surgery (time 2) from 55 patients who received NACT with anthracycline/taxane. Gut microbiome was analyzed by 16S rRNA amplicon sequencing to characterize the α (InvSimpson index) and β (weighted UniFrac distance metric) diversity, as well as taxonomic composition. Clinicopathologic prognostic factors were retrieved from medical records. Pathological complete response (pCR) was defined as the absence of invasive carcinoma in breast and axillary nodes (ypT0/Tis ypN0). Stromal tumor-infiltrating lymphocytes (sTIL) were reported according to the TIL working group criteria. Information about prior use (&amp;lt; 60 days before stating on NACT) of antibiotic (ATB) was obtained directly from patients. Statistical significance was set at P ≤ 0.05 and analysis of composition of microbiomes (ANCOM-BC2) was used to identify enriched genera with p-values adjusted using FDR correction ≤ 0.25. Results: Median age was 49 years (range 31-73). Eleven patients (20%) reported prior antibiotic use at baseline. About 34.5% of patients had HR+/HER2- tumors, 45.4% had triple negative breast cancer (TNBC), and 20% had HER2-positive breast cancer. Fourteen (25%) patients achieved a pCR. Out of 55, 47 (85.4%) had sTIL information. There was no significant difference in alpha diversity (p = 0.6) or beta-diversity (p = 0.8) between the pCR and residual disease group nor within clinical pathologic factors (age, staging, histological tumor grade, subtype of breast cancer based on IHC, sTIL). The most abundant taxon in both time 1 and time 2 were the same (Blautia at genus level, Lachnospiraceae at family level, and Lachnospirales at order level), and longitudinal samples collected during NACT showed no significant changes in GM composition. At baseline, we found an enrichment for Clostridia sp. among patients who did not use ATB (p &amp;lt; 0.05, pFDR ≤ 0.25). Additionally, we found enrichment for Bifidobacterium (p &amp;lt; 0.05, pFDR ≤ 0.25) among patients with HER2 subtype who presented residual disease. Conclusions: Gut microbiome analysis in early breast cancer is feasible and to our knowledge, this is the first study to evaluate the intestinal microbiota of Brazilian patients with breast cancer. We did not observe any significant association between GM diversity and taxonomic composition with clinical pathologic factors and pCR in this study, nor did we observe changes in the ecological balance of the GM following NACT in breast cancer. Further studies are needed to explore the potential influence of the gut microbial ecosystem on tumor biology and response to neoadjuvant chemo-immunotherapy. Citation Format: Ludmila Thommen, Vitor Heidrich, Rosângela Vieira de Andrade, Luiza Nardin Weis, Maria Sueli Soares Felipe, Melissa Lole Da Cas Vita, Thiago David Alves Pinto, Anamaria Camargo, Romualdo Barroso-Sousa. Characterization of Gut Microbiome of patients with early-stage breast cancer treated with neoadjuvant chemotherapy [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-03-04.

Abstract PO2-02-02: BREAst Cancer Personalized NuTrition (BREACPNT): dietary intervention in HR+ breast cancer patients treated with endocrine therapy

Abstract BACKGROUND Breast cancer patients treated with adjuvant endocrine therapy commonly experience weight gain, which has been associated with low adherence to therapy and worse breast cancer prognosis. Dietary interventions are the first-line treatment for weight management in breast cancer patients and have beneficial results. Yet, the ability to maintain these outcomes requires further research. Here, we aimed to assess whether a personalized postprandial glucose targeting (PPT) diet is beneficial for weight management and metabolic health as compared with the recommended Mediterranean (MED) diet in this population. DESIGN AND METHODS BREACPNT is a phase-2 randomized trial in HR+ patients with breast cancer, treated with adjuvant endocrine therapy. We randomly assigned participants to follow a MED diet or a PPT diet for a 6-month dietary intervention and additional 6-month follow-up. The PPT diet is based on a machine-learning algorithm that integrates clinical and microbiome features to predict personal postprandial glucose responses (PPGRs). During the intervention, participants were monthly followed by a registered dietitian, they were additionally connected to a 2-week continuous glucose monitoring (CGM) on 3-timepoints, provided stool and blood samples and self-reported dietary intake using a smartphone application. RESULTS Among 127 randomized patients (mean ± SD age 53 ± 10 years, BMI 28.6 ± 5 kg/m2), 103 (81%) completed the 6-month intervention period. A total of 94 participants provided 12-month follow-up data. Both interventions led to a significant weight loss. The PPT-diet showed numerically greater weight loss with median change of -1.45kg (IQR -3.75 – 0) compared to the MED-diet with median change of -1kg (IQR -3.2 - 0.1) , however this was not significant (p=0.9). Notably, at the 12-month time point , participants in the PPT arm were more likely to maintain the weight loss (median -1.2kg, IQR -4 - 0.1) compared to participants in the MED-arm (median -0.15kg , IQR -4.25 - 1.5), p=0.14) and had significantly improved waist circumference (median, IQR; -5 cm, -8-(-2) in the PPT arm, compared to -1cm, -6.5-3 in the MED arm, p=0.01). In terms of glucose metabolism the PPT-diet led to improved glycemic control as measured by CGM, with significant lower average postprandial glucose responses (PPGRs) and glucose coefficient of variation (CV) compared to the MED-diet arm (mean 6-month change in PPGR was 2.1 ± 7.5 mg/dL × h for MED and −3.4 ± 5.6 mg/dL × h for PPT, p&amp;lt; 0.001, and the 6-month mean change for CV was 0.15 ± 2.76 for MED and −1.37 ± 3.2 for PPT, p&amp;lt; 0.01). Within the entire cohort, participants who experienced the greatest weight loss (upper quartile) were more likely to be postmenopausal compared to participants in the lower quartile. Additionally, participants who did not achieve weight loss (lower quartile) were significantly more likely to be treated with tamoxifen than AI (p=0.015). CONCLUSIONS In this dietary intervention in HR+ breast cancer patients, both PPT diet and MED diet led to weight loss and improved food quality, with a slight advantage to PPT diet. PPT diet additionally improved glycemic features as compared to MED diet, which are linked to lower risk of obesity and disease recurrence, suggesting an advantage in a glucose targeting approach. Premenopausal and Tamoxifen treated patients were less likely to lose weight through the intervention. These findings may have implications for dietary advice in clinical practice. Citation Format: Michal Rein, Maya Dadiani, Anastasia Godneva, Michal Bakalenik-Gavry, Dana Morzaev-Sulzbach, Maya Lotan-Pompan, Adina Weinberger, Eran Segal, Einav Gal-Yam. BREAst Cancer Personalized NuTrition (BREACPNT): dietary intervention in HR+ breast cancer patients treated with endocrine therapy [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-02-02.

Substitution of One Meat-based meal with Vegetarian and Vegan Alternatives Generates Lower Ammonia and Alters Metabolites in Cirrhosis: A Randomized Clinical Trial.

Diet can affect ammoniagenesis in cirrhosis and hepatic encephalopathy (HE) but the impact of dietary preferences on metabolomics in cirrhosis is unclear. As most Western populations follow meat-based diets, we aimed to determine the impact of substituting a single meat-based meal with an equal protein-containing vegan/vegetarian alternative on ammonia & metabolomics in outpatients with cirrhosis on a meat-based diet. Outpatients with cirrhosis with and without prior HE on a stable Western meat-based diet were randomized 1:1:1 into 3 groups. Patients were given a burger with 20g protein of either meat, vegan (V) or vegetarian (VG). Blood for metabolomics via liquid chromatography-mass spectrometry and ammonia was drawn at baseline and hourly for 3 hours post-meal while patients under observation. Stool microbiome characteristics, changes in ammonia, and metabolomics were compared between/within groups. Stool microbiome composition was similar at baseline. Serum ammonia increased from baseline in the meat group but not the VG or V group. Metabolites of branched chain and acyl-carnitines decreased in the meat group compared to non-meat groups. Alterations in lipid profile (higher sphingomyelins and lower lysophospholipids) were noted in the meat group when compared to V and VG groups. Substitution of a single meat-based meal with a non-meat alternatives results in lower ammoniagenesis and altered serum metabolomics centered on branched-chain amino acids, acylcarnitines, lysophospholipids, and sphingomyelins in patients with cirrhosis regardless of HE or stool microbiome. Intermittent meat substitution with vegan or vegetarian alternatives could be helpful in reducing ammonia generation in cirrhosis.