Operational Taxonomic Unit Level Research Articles

Impact of Lactobacillus- and Bifidobacterium-Based Direct-Fed Microbials on the Performance, Intestinal Morphology, and Fecal Bacterial Populations of Nursery Pigs.

Weaning is a critical stage in the swine production cycle, as young pigs need to adjust to sudden and dramatic changes in their diet and environment. Among the various organ systems affected, the gastrointestinal tract is one of the more severely impacted during this transition. Traditionally, challenges at weaning have been managed by prophylactic use of antibiotics, which not only provides protection against diarrhea and other gut dysfunction but also has growth-promoting effects. With banning or major restrictions on the use of antibiotics for this purpose, various alternative products have been developed as potential replacements, including direct-fed microbials (DFMs) such as probiotics and postbiotics. As their efficiency needs to be improved, a continued effort to gain a deeper understanding of their mechanism of action is necessary. In this context, this report presents a study on the impact of a Lactobacillus-based probiotic (LPr) and a Bifidobacterium-based postbiotic (BPo) when added to the diet during the nursery phase. For animal performance, an effect was observed in the early stages (Day 0 to Day 10), as pigs fed diets supplemented with either DFMs were found to have higher average daily feed intake (ADFI) compared to pigs fed the control diet (p < 0.05). Histological analysis of intestinal morphology on D10 revealed that the ileum of supplemented pigs had a higher villus height/crypt depth ratio (p < 0.05) compared to controls, indicating a benefit of the DFMs for gut health. In an effort to further explore potential mechanisms of action, the effects of the DFMs on gut microbial composition were investigated using fecal microbial communities as a non-invasive representative approach. At the bacterial family level, Lactobacillaceae were found in higher abundance in pigs fed either LPr (D10; p < 0.05) or BPo (D47; p < 0.05). At the Operational Taxonomic Unit (OTU) level, which can be used as a proxy to assess species composition, Ssd-00950 and Ssd-01187 were found in higher abundance in DFM-supplemented pigs on D47 (p < 0.05). Using nucleotide sequence identity, these OTUs were predicted to be putative strains of Congobacterium massiliense and Absicoccus porci, respectively. In contrast, OTU Ssd-00039, which was predicted to be a strain of Streptococcus alactolyticus, was in lower abundance in BPo-supplemented pigs on D47 (p < 0.05). Together, these results indicate that the DFMs tested in this study can impact various aspects of gut function.

Abstract 6204: Differential gut microbiome alpha diversity in endometrial and ovarian carcinoma patients

Abstract Background: Emerging research underscores the gut microbiome's critical role in cancer development, progression, and response to treatment. As a part of the “ASAP” study, which focuses on the implementation of comprehensive molecular profiling and deep clinical annotation of electronic health records in participants diagnosed with or at risk of developing cancer, we have established a microbiome-associated biobank and corresponding clinical dataset to systematically explore the dynamics of the gut microbiome as patients progress through cancer treatment. We describe a pilot project where we explore the baseline microbiome samples collected from ASAP participants, particularly from those with endometrial and ovarian carcinomas. Methods: Stool samples from patients were collected at the time of enrollment in the ASAP study and sampling is repeated every three months to align with the additional biosampling procedures. Microbial DNA was extracted from the baseline stool samples and subjected to sequencing of the V4 region of the 16S rRNA gene. After generating species level operational taxonomic units (OTUs), alpha diversity measures were generated in the form of the inverse Simpson index. In order to determine whether there was a difference in alpha diversity between individuals with ovarian (N = 37) and endometrial (N = 35) carcinomas, we employed a t-test with 100,000 permutations to derive an empirical p-value. Results: We present sequencing results from the initial n=297 samples. Our comparison of the alpha diversity between ASAP study participants with ovarian and endometrial carcinomas showed a significant difference between the two groups, with the ovarian cancer patients having a lower alpha diversity (empirical p-value = 0.03915). Due to the uniform sampling, biobanking, and analytical procedures, our study allows the ability to explore microbiome features amongst various cancer diagnoses while minimizing laboratory and analytical differences that plague microbiome reproducibility. Conclusions: We observed a significant difference in alpha diversity between patients with endometrial and ovarian carcinomas. Although the current results are preliminary, the wealth of information available in the ASAP protocol will allow us to continue exploring the association of the gut microbiome with cancer and the associated treatment. Citation Format: Casey T. Finnicum, Tobias Meissner, Christel Davis, Sarah Viet, Jason L. Petersen, McKenna Deaton, Benjamin Solomon, William Spanos, David Starks, Rachel Elsey, Erik A. Ehli, Casey Williams. Differential gut microbiome alpha diversity in endometrial and ovarian carcinoma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6204.

Afforestation alters soil microbial community composition and reduces microbial network complexity in a karst region of Southwest China

AbstractSoil microbial community plays important roles in altering ecological processes and biogeochemical cycles in ecosystems. However, little is known about how afforestation influences the diversity, composition, and ecological network of soil microbial community in karst regions. In this study, soil samples were collected from one farmland (FL) and three afforestation lands including one bamboo forest (BA), one landscape tree planting forest (LAT), and one orange orchard (ORO) in a karst region of Southwest China. The bacterial and fungal communities were characterized using the high‐throughput sequencing approach, and soil properties including soil organic carbon, pH, soil water content, and soil total and available nutrient contents were measured under different land use treatments. Results showed that conversion from FL to BA and LAT significantly reduced the Shannon diversity of bacterial community. At the phylum level (top 10), genus level (top 30), and operational taxonomic units (OTUs) level, afforestation from FL resulted in significant changes in nine phyla, 24 genera, and 31.32% OTUs of bacterial community, and in three phyla, 13 genera, and 11.62% OTUs of fungal community. The number of nodes, number of negative edges, connectivity, average degree, and relative modularity of the microbial network under afforestation lands decreased by 9.33%–18.66%, 47.98%–72.75%, 0.45%–5.93%, 14.73%–22.29%, and 6.46%–23.50%, respectively, compared with FL. The soil organic carbon, total potassium and total phosphorus were identified as the key soil properties affecting the microbial community. Compared with LAT and ORO, the changes in bacterial and fungal communities under BA were more obvious because of the higher contents in soil organic carbon (13.48%) and total potassium (27.18%). In conclusion, afforestation significantly changed compositions and ecological network complexity of soil microbial community in karst regions, and conversion from FL to BA had stronger influences on the changes of soil microbial community than other afforestation lands in Southwest China. These findings provide the context necessary to evaluate the responses of soil microbial community to land use changes in karst regions.

Endophytic Fungal Diversity of Mangrove Ferns Acrostichum speciosum and A. aureum in China.

Microbial communities are an important component of mangrove ecosystems. In order to reveal the diversity of endophytic fungi in the mangrove ferns Acrostichum speciosum and A. aureum in China, the internal transcribed spacer (ITS) regions of endophytic fungi in four plant tissues (leaves, petioles, roots, and rhizomes) from three locations (Zhanjiang, Haikou, and Wenchang) were sequenced. The richness, species composition, and community similarity were analyzed. The main results are as follows: the dominant fungi in A. speciosum and A. aureum belonged to the phyla Ascomycota and Basidiomycota, accounting for more than 75% of the total identified fungi; in terms of species composition at the operational taxonomic unit (OTU) level, the endophytic fungi in A. aureum were more diverse than those in A. speciosum, and the endophytic fungi in rhizomes were more diverse than in other tissues. In Zhanjiang, both A. speciosum and A. aureum showed the richest diversity of endophytic fungi, both at the OTU classification level and in terms of species composition. Conversely, the richness of endophytic fungi in the samples of A. speciosum from Wenchang and Haikou is extremely low. The regional differences in dominant fungi increase with the degrading of taxonomic levels, and there were also significant differences in the number of unique fungi among different origins, with Zhanjiang samples having a larger number of unique fungi than the other locations. There were significant differences in the dominant fungi among different tissues, with Xylariales being the dominant fungi in rhizomes of A. speciosum and Hypocreales being the dominant fungi in the petioles, roots, and rhizomes of A. aureum. Overall, the community similarity of endophytic fungi among locations is moderately dissimilar (26-50%), while the similarity between tissues is moderately similar (51-75%). The low diversity of endophytic fungi could be one of the main reasons for the endangerment of A. speciosum. The protection of the diversity of endophytic fungi in the underground parts of A. speciosum is essential for the conservation of this critically endangered mangrove fern.

Identification of keystone taxa in root canals and periapical lesions of post-treatment endodontic infections: Next generation microbiome research.

The aim of this study was to analyse and compare the microbiome present in root canals and periapical lesions of teeth with post-treatment infections, and to identify the presence of keystone taxa in both habitats using next-generation sequencing analysis. Apices and periapical lesions of patients with post-treatment apical periodontitis were surgically extracted. Specimens were cryo-pulverized, bacterial DNA was extracted, and the V3-V4 hypervariable regions of the 16S rRNA gene were sequenced using the Illumina Miseq platform. Bioinformatic analysis was carried out with Mothur software, whilst diversity indices were obtained using operational taxonomic units (OTUs). The diversity indices were compared with the Kruskal-Wallis test, and community composition differences were explored with Permutational Multivariate Analysis of Variance (PERMANOVA). A bacterial functional study was performed with the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis. Co-occurrence network analyses were performed using the Sparse Correlations for Compositional data (SparCC). Eigencentrality, clr-based abundance and ubiquitousness were applied to infer keystone taxa. P values <.05 were considered statistically significant. Thirty-two apices and thirty-nine periapical lesions were sequenced and analysed. A similar alpha-diversity (p < .05) and community composition (p = .91) was observed for apices and lesion samples. The most abundant OTUs identified amongst all samples included Fusobacterium nucleatum, Prevotella loescheii, Streptococcus intermedius, Porphyromonas gingivalis, Parvimonas micra, Synergistetes bacterium, Tannerella forsythia and Peptostreptococcus stomatis. The metabolic pathways with >0.81% abundances included membrane transport, genetic information processing and metabolic pathways. F. nucleatum was identified as a keystone taxon as it showed ubiquitousness, an eigenvector centrality value of 0.83 and a clr-based abundance >4. The microbiome in apices and periapical lesions of post-treatment endodontic infections showed a similar diversity and taxonomic composition. Co-occurrence network analyses at OTU level identified F. nucleatum as a keystone taxon candidate in these infections.

The response of gut and fecal bacterial communities of the European sea bass (Dicentrachus labrax) fed a low fish-plant meal and yeast protein supplementation diet

Abstract As aquaculture is nowadays the major fish-food production sector, continuous research is undergoing for aquafeeds that could replace conventional fishmeal in order to enhance its environmental and economic sustainability. Fish gut microorganisms might be involved in nutrient assimilation and thus they are crucial for their hosts’ well-being. In this study, the bacterial diversity was investigated by16S rRNA gene metabarcoding in order to investigate changes in midgut (M) and feces (F) microbiota of sea bass Dicentrachus labrax fed with conventional (C) and innovative-low fish meal diet (I), aiming at discovering microbiota that could be associated with the enhancement of host's health and productivity. Our results indicated that Proteobacteria (Pseudomonadota) prevailed in all samples followed by Firmicutes (Bacillota) or Bacteroidota (mostly in feces), while fecal communities were richer. Taxonomic distributions at the operational taxonomic unit level in midgut samples revealed differentially abundant fermentative species that prevailed in individuals fed with the innovative diet. Especially Staphylococcus was more abundant in MI samples implying enhancement from ingredients present only in the innovative diet and implying that this feed shapes rather favorable microbiota, which could support the digestion and good growth performance in aquaculture.

Seasonal dynamics of phyllosphere epiphytic microbial communities of medicinal plants in farmland environment.

The phyllosphere of plants is inhabited by various microorganisms, which play a crucial role in plant physiological metabolism. Currently, there is limited research on the dynamic effects of species and seasons on plant phyllosphere microbial community diversity and microbial interactions. In this study, high-throughput sequencing technology was used to sequence the leaf surface parasitic microorganisms of five medicinal plants (Bupleurum chinense, Atractylodes lancea, Salvia miltiorrhiza, Astragalus membranaceus, and Lonicera japonica). The results showed that bacteria and fungi clustered into 3,898 and 1,572 operational taxonomic units (OTUs), respectively. Compared to host species, seasons had a more significant impact on the a diversity of bacteria and fungi. The heterogeneity of phyllosphere microbial communities was greater in winter compared to summer. Key species analysis at the OTU level and Spearman correlation analysis demonstrated significant preferences in microbial interactions under plant and seasonal backgrounds. The network connections between bacterial and fungal communities significantly increased during seasonal transitions compared to connections with plants. This study enhances our understanding of the composition and ecological roles of plant-associated microbial communities in small-scale agricultural environments. Additionally, it provides valuable insights for assessing the biodiversity of medicinal plants.

Specific gut microbiome signature predicts hepatitis B virus-related hepatocellular carcinoma patients with microvascular invasion

Background We aimed to assess differences in intestinal microflora between patients with operable hepatitis B virus-related hepatocellular carcinoma (HBV-HCC) with microvascular invasion (MVI) and those without MVI. Additionally, we investigated the potential of the microbiome as a non-invasive biomarker for patients with MVI. Methods We analyzed the preoperative gut microbiomes (GMs) of two groups, the MVI (n = 46) and non-MVI (n = 56) groups, using 16S ribosomal RNA gene sequencing data. At the operational taxonomic unit level, we employed random forest models to predict MVI risk and validated the results in independent validation cohorts [MVI group (n = 17) and non-MVI group (n = 15)]. Results β diversity analysis, utilizing weighted UniFrac distances, revealed a significant difference between the MVI and non-MVI groups, as indicated by non-metric multidimensional scaling and principal coordinate analysis. We also observed a significant correlation between the characteristic intestinal microbial communities at the genus level and their main functions. Nine optimal microbial markers were identified, with an area under the curve of 79.76% between 46 MVI and 56 non-MVI samples and 79.80% in the independent verification group. Conclusion This pioneering analysis of the GM in patients with operable HBV-HCC with and without MVI opens new avenues for treating HBV-HCC with MVI. We successfully established a diagnostic model and independently verified microbial markers for patients with MVI. As preoperative targeted biomarkers, GM holds potential as a non-invasive tool for patients with HBV-HCC with MVI.

Enhanced trimethylamine metabolism and gut dysbiosis in type 2 diabetes mellitus with microalbumin.

Abnormal gut microbiota and blood trimethylamine-N-oxide (TMAO) metabolome have been reported in patients with type 2 diabetes mellitus (T2DM) and advanced diabetic nephropathy. This study aimed to investigate the gut microbiota profiles and a group of targeted urine metabolic characteristics in T2DM patients with or without microalbuminuria, to determine the correlation between the gut microbiota composition, trimethylamine (TMA) metabolism, and the clinical features during progression of diabetic kidney disease (DKD). This study included 26 T2DM patients with microalbuminuria (Micro), 26 T2DM patients with normoalbuminuria (Normo), and 15 healthy controls (HC). Urine and Fecal samples were detected using ultra performance liquid chromatography tandem mass spectrometry and 16S ribosomal DNA gene sequencing, respectively. The TMAO/TMA ratio decreased gradually during the HC-Normo-Micro transition. The levels of TMA, choline and betaine were significantly different between the HC group and the T2DM patients belonging to both Normo and Micro groups. At the operational taxonomic unit (OTU) level, the gut microflora diversity was significantly reduced in the Micro groups compared to the HC groups and the Normo groups. Taxonomic analyses revealed significant consumption in the relative abundances of eight bacterial genera and significant enrichment of two bacterial genera during the HC-Normo-Micro transition. Furthermore, the relative abundances of six bacterial genera, namely, Ruminococcus_1, [Eubacterium]_ruminantium_group, Roseburia, Faecalibacterium, Fusicatenibacter and Coprococcus_3 exhibited significant differences, and were associated with elevated urinary albumin creatinine ratio (UACR), TMAO/TMA, TMA and its precursors in the Micro group compared with the other groups. The imbalance of gut microbiota has occurred in patients with early-stage DKD, and the consumption of short-chain fatty acid-producing bacteria were associated with the accumulation of TMA and UACR.

Profile of Pancreatic and Ileal Microbiota in Experimental Acute Pancreatitis.

Acute pancreatitis (AP) is accompanied by gut microbiota dysbiosis. However, the composition of the pancreatic and ileal microbiota associated with AP is still unknown. This study aims to examine the alterations in the microbial composition of the pancreas and ileum in the context of experimental acute pancreatitis, as well as explore the potential interplay between these two regions. Methods: Caerulein (CAE), caerulein+lipopolysaccharide (CAE+LPS), and L-arginine (ARG) were used to induce AP in mice. The pancreas and ileum were collected for histological study and bacterial 16S rRNA gene sequencing. The results showed microbial structural segregation between the AP and control groups and between ARG and the two CAE groups (CAE, CAE+LPS) in the pancreas and ileum. Taxonomic analysis at the genus level and linear discriminant analysis effect size (LEfSe) at the operational taxonomic units (OTUs) level illustrated that AP mice exhibited a marked increase in the relative abundance of Muribaculaceae and a decrease in that of Dietzia both in the pancreas and ileum, and a reduction in Bifidobacterium only in the ileum; in addition, Roseburia was enriched in the two CAE groups in the pancreas and/or ileum, while Escherichia-Shigella expanded in the pancreas of the ARG group. Spearman correlation analysis between pancreatic and ileal microbiota revealed that the abundance of Muribaculaceae and Dietzia in the pancreas was related to that in the ileum. These findings demonstrated that caerulein and L-arginine differentially disturbed the pancreatic and ileal microbiota when inducing AP. Furthermore, these findings provide preliminary support for an association between the microbiota of the pancreas and ileum, which could be caused by AP-induced microbial translocation.

Effects of Heated Drinking Water during the Cold Season on Serum Biochemistry, Ruminal Fermentation, Bacterial Community, and Metabolome of Beef Cattle.

This study explored the effects of drinking heated water in the cold seasons on the serum metabolism, rumen microbial fermentation, and metabolome of beef cattle. Twelve fattening cattle (642 ± 14.6 kg) aged 21 to 22 months were randomly and equally divided into two groups based on body weight: one receiving room-temperature water (RTW; average 4.39 ± 2.55 °C) and the other heated water (HW; average 26.3 ± 1.70 °C). The HW group displayed a significant decrease in serum glucose (p < 0.01) and non-esterified fatty acid (p < 0.01), but increases in insulin (p = 0.04) and high-density lipoprotein (p = 0.03). The rumen fermentation parameters of the HW group showed substantial elevations in acetate (p = 0.04), propionate (p < 0.01), isobutyrate (p = 0.02), and total volatile fatty acids (p < 0.01). Distinct bacterial composition differences were found between RTW and HW at the operational taxonomic unit (OTU) level (R = 0.20, p = 0.01). Compared to RTW, the HW mainly had a higher relative abundance of Firmicutes (p = 0.07) at the phylum level and had a lower abundance of Prevotella (p < 0.01), norank_f_p-215-o5 (p = 0.03), and a higher abundance of NK4A214_group (p = 0.01) and Lachnospiraceae_NK3A20_group (p = 0.05) at the genus level. In addition, NK4A214_group and Lachnospiraceae_NK3A20_group were significantly positively correlated with the rumen propionate and isovalerate (r > 0.63, p < 0.05). Prevotella was negatively correlated with rumen propionate and total volatile fatty acids (r = -0.61, p < 0.05). In terms of the main differential metabolites, compared to the RTW group, the expression of Cynaroside A, N-acetyl-L-glutamic acid, N-acetyl-L-glutamate-5-semialdehyde, and Pantothenic acid was significantly upregulated in HW. The differentially regulated metabolic pathways were primarily enriched in nitrogen metabolism, arginine biosynthesis, and linoleic acid metabolism. Prevotella was significantly positively correlated with suberic acid and [6]-Gingerdiol 3,5-diacetate (r > 0.59, p < 0.05) and was negatively correlated with Pantothenic acid and isoleucyl-aspartate (r < -0.65, p < 0.05). NK4A214_group was positively correlated with L-Methionine and glycylproline (r > 0.57, p < 0.05). Overall, our research demonstrates the important relationship between drinking water temperature and metabolic and physiological responses in beef cattle. Heating drinking water during cold seasons plays a pivotal role in modulating internal energy processes. These findings underscore the potential benefits of using heated water as a strategic approach to optimize energy utilization in beef cattle during the cold seasons.

Mycorrhizal Fungal Diversity Associated with Six Understudied Ectomycorrhizal Trees in the Republic of Korea.

Mycorrhizal fungi are key components of forest ecosystems and play essential roles in host health. The host specificity of mycorrhizal fungi is variable and the mycorrhizal fungi composition for the dominant tree species is largely known but remains unknown for the less common tree species. In this study, we collected soil samples from the roots of six understudied ectomycorrhizal tree species from a preserved natural park in the Republic of Korea over four seasons to investigate the host specificity of mycorrhizal fungi in multiple tree species, considering the abiotic factors. We evaluated the mycorrhizal fungal composition in each tree species using a metabarcoding approach. Our results revealed that each host tree species harbored unique mycorrhizal communities, despite close localization. Most mycorrhizal taxa belonged to ectomycorrhizal fungi, but a small proportion of ericoid mycorrhizal fungi and arbuscular mycorrhizal fungi were also detected. While common mycorrhizal fungi were shared between the plant species at the genus or higher taxonomic level, we found high host specificity at the species/OTU (operational taxonomic unit) level. Moreover, the effects of the seasons and soil properties on the mycorrhizal communities differed by tree species. Our results indicate that mycorrhizal fungi feature host-specificity at lower taxonomic levels.

Comparison of the nutrient value, nonspecific immunity, and intestinal microflora of red swamp crayfish (Procambarus clarkii) in different culture modes

This study aimed to compare the nutritional composition, digestive enzyme activity, nonspecific immunity, and intestinal microflora of Procambarus clarkii under different culture modes: crayfish and crab coculture, pond intensive farmed culture (PF), rice and crayfish coculture (RC), cement pond culture (CP), and wild-caught. The muscle, hepatopancreas, and intestine of crayfish with a mean weight of 25.35 ± 4.23 g were collected and examined. The results showed that the nutritive value of amino acids and fatty acids in the muscle was higher in the RC group than in the other groups. Moreover, muscle crude protein contents were the highest in the CP group. Trypsin activities in the intestines were significantly higher in the PF and CP groups than in the other groups (P < 0.05). The alkaline phosphatase (AKP) and acid phosphatase (ACP) activities of the PF group were the lowest, whereas the CP group showed high AKP and ACP activities and low malondialdehyde levels. The dominant bacterial communities in the intestine of P. clarkii included Proteobacteria, Bacteroidetes, Firmicutes, RsaHF231, Tenericutes, and Planctomycetes at the phylum level and ZOR0006, Candidatus Bacilloplasma, and Aeromonas at the genus level. These results suggested that the dominant bacterial community phyla and genera in the intestine varied greatly between the culture modes. The results of principal coordinate analysis based on the operational taxonomic unit level showed that the bacterial community distribution in the CP group was quite different from that in the other groups, indicating dramatic variations in species diversity. Our current findings will provide a theoretical foundation for understanding the association between the culture modes of P. clarkii and nutrition, immunity, and intestinal microflora.

Comparison of the gut microbiota and untargeted gut tissue metabolome of Chinese mitten crabs (Eriocheir sinensis) with different shell colors.

The Chinese mitten crab (Eriocheir sinensis) is a highly valued freshwater crustacean in China. While the natural shell color of E. sinensis is greenish brown (GH), we found a variety with a brownish-orange shell color (RH). Although RH is more expensive, it exhibits a lower molting frequency and growth rate compared with GH, which significantly reduces its yield and hinders large-scale farming. The growth and development of animals are closely related to their gut microbiota and gut tissue metabolic profiles. In this study, we compared the gut microbiome communities and metabolic profiles of juvenile RH and GH crabs using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC-MS), respectively. Our findings indicated that the intestinal microbial composition and metabolic characteristics of E. sinensis differed significantly between RH and GH. At the operational taxonomic unit (OTU) level, the α-diversity of the gut microbiota did not differ significantly between RH and GH, while the β-diversity of the RH gut microbiota was higher than that of the GH gut microbiota. At the species level, the richness of unclassified_c_Alphaproteobacteria was significantly higher in the GH group, while the RH group had a significantly higher richness of three low-abundance species, Flavobacteria bacterium BAL38, Paraburkholderia ferrariae, and uncultured_bacterium_g__Legionella. In the current study, 598 gut tissue metabolites were identified, and 159 metabolites were significantly different between GH and RH. The metabolite profile of RH was characteristic of a low level of most amino acids and lipid metabolites and a high level of several pigments compared with that of GH. These metabolites were enriched in 102 KEGG pathways. Four pathways, including (1) Central carbon metabolism in cancer, (2) protein digestion and absorption, (3) alanine, aspartate and glutamate metabolism, and (4) aminoacyl-tRNA biosynthesis, were significantly enriched. The correlation analysis between metabolites and microbiotas indicated that most key differential metabolites were positively correlated with the abundance of Shewanella_sp_MR-7. This research provided a greater understanding of the physiological conditions of E. sinensis varieties with different shell colors by comparing the gut microbiota and gut tissue metabolome.

Microbiome, socioeconomic status (SES), fiber intake, and response to checkpoint inhibitor therapy in patients with non-small cell lung cancer (NSCLC): A pilot study.

e14710 Background: Lung cancer affects a disproportional number of socioeconomically disadvantaged patients (pts). Responses to checkpoint inhibitor therapy (CIT) vary. Microbiome diversity may correlate with benefit from CIT. High fiber diets lead to microbiome diversity. We hypothesize that unexplained lung cancer disparities may be in part due to differences in microbiome diversity determined by unhealthy dietary patterns dictated by lower SES. Methods: Following IRB review, 25 pts with metastatic NSCLC starting CIT-based treatment were enrolled. Pre-treatment oral and fecal samples were collected. 24-hour dietary recalls were obtained. SES index was calculated based on education, employment, housing and annual income. High fiber intake was defined as &gt; 20 g/day. Best treatment response per RECIST 1.1 was assessed. Microbial 16s rRNA were sequenced with Illumina MiSeq platform. Sequence analyses utilized QIIME 2 with DADA2 plugin. Taxonomic assignments used the Greengenes database. Microbiome composition was analyzed by calculating alpha diversity (Chao1, Shannon diversity and Simpson index), beta diversity and differential abundance of microbial compositions. Hierarchical linear model was constructed for each SES variable with and without biological covariates. Results: Pts with samples &gt;1000 operational taxonomic unit (OTU) levels were included (N = 22) in the analysis. 50% were male, median age was 71, 36% (8/22) were of Black race and 23% (5/22) were of low SES. Median fiber intake was 11.9 grams. Males had higher alpha diversity than females (p=.038). Pts with high fiber intake had greater fecal Proteobacteria compared to low fiber intake pts (p&lt;0.05). Bacteroides and Firmicutes fecal levels were significantly different for all pts compared to Human Microbiome Project (HMP) reported normal levels (p&lt;0.01). Actinobacteria and Proteobacteria levels for low-fiber intake pts were also significantly elevated compared to HMP normal levels (p&lt;0.05). There were no differences observed in microbiome when comparing SES index. However, high SES index patients had elevated fecal levels of Actinobacteria, Firmicutes and Proteobacteria and lower levels of Bacteroides compared to HMP levels. There was a trend towards higher alpha diversity of oral samples in partial responders pts compared to those with stable or progression of the disease (p=0.08). Conclusions: Pts with metastatic NSCLC exhibited different microbial composition compared to HMP normal levels. Associations between SES and microbial distribution in such pts warrant further investigation. Increased sample size is needed to better determine differences in oral microbiome in responders to immunotherapy and better evaluate the role of sex in this setting.

Dissecting biodiversity: assessing the taxonomic, functional and phylogenetic structure of an insect metacommunity in a river network using morphological and metabarcoding data

Most empirical metacommunity studies rely solely on morphological identification of taxa, precluding the species-level identification of several biotic groups, which can influence the characterization of metacommunities. DNA metabarcoding enables inference of species and even intraspecific diversity from community samples but has rarely been used to infer metacommunity structure. Here, we combined morphology and metabarcoding to improve the characterization of an insect metacommunity at different identification levels. We included measures of taxonomic, functional and phylogenetic richness, and we evaluated drivers affecting metacommunity structure (i.e., environmental filtering and dispersal). Communities were sampled from an area that included nine perennial, two near-perennial and two intermittent sites in a river network characterized by high hydrological variability. We identified organisms to a mixed (family to species) taxonomic level using morphology, and to operational taxonomic unit (OTU) and haplotype levels using metabarcoding of the mitochondrial cytochrome c oxidase gene. Diptera and Ephemeroptera showed the greatest increases in taxonomic and phylogenetic richness but not biological trait richness with increasing taxonomic resolution. The joint effect of environmental filtering and dispersal was more important than their individual effects in shaping metacommunity structure at all identification levels. Mixed-level and OTU-level identification were more effective than family and haplotype in characterizing the drivers of metacommunity structure. We demonstrate that the greater taxonomic resolution enabled by metabarcoding could improve understanding of metacommunities within river networks, thus enhancing our capacity to predict ecological responses in ecosystems adapting to global change.

Associations of soil bacterial diversity and function with plant diversity in Carex tussock wetland.

Some species of Carex can form tussocks, which are usually distributed in valleys and flood plains. The soil microbial community diversity and function of micro-habitats formed by tussocks are associated with plant diversity, and research on these associations can guide Carex tussock wetland restoration. In this study, we selected tussock wetlands dominated by Carex appendiculata, including natural wetlands (NW), artificially restored wetlands (ARW), and naturally restored wetlands (NRW), and investigated plant diversity. Soil samples were collected from the quadrats of each sample plot with the maximum (ma), median (me), and minimum (mi) plant Shannon index values, and high-throughput sequencing was used to analyze the bacterial community composition, diversity, and functions. The plant diversity indexes of neither ARW nor NRW significantly differed from that of NW, but the companion species in NRW were hygrophytes and mesophytes, in contrast to only hygrophytes serving as companion species in NW and ARW. The soil bacterial communities at the operational taxonomic unit level of the nine quadrats with different plant Shannon index values significantly (p < 0.01) differed. The relative abundances of the dominant phyla (Proteobacteria, Chloroflexi, and Bacteroidetes) and the dominant genera (Geobacter, Sideroxydans, and Clostridium except for unassigned genera) significantly (p < 0.05) differed under the different levels of plant diversity. The plant Shannon index, soil moisture content, total organic carbon, N, and P were significantly (p < 0.05 or p < 0.01) correlated with the bacterial Shannon index. The phylogenetic diversity of the bacterial community in NW was significantly (p < 0.0001) different from those in ARW and NRW, and that in ARW was also significantly (p < 0.05) different from that in NRW. The functional groups of bacterial communities associated with plant diversity. In the NWme, ARWme, and NRWme bacterial communities, the relative proportions of functional groups related to soil N cycle were higher, but those related to soil S and C cycles were lower. Considering the rehabilitation of both plant and microbial communities, the methods used for establishing the ARW are recommended for Carex tussock wetland restoration.

Negative Linear or Unimodal: Why Forest Soil Fungal Latitudinal Diversity Differs across China.

To identify the reasons for the inconsistency in patterns of latitudinal gradients of forest soil fungal biodiversity in China, a reanalysis of data was performed. Causes are linked to the different environments of continents and islands and the inconsistency between different classification standards. The following three suggestions are made for future studies: sites on the mainland and islands should be distinguished in these types of studies, the Shannon index should be used to represent fungal diversity instead of operational taxonomic unit (OTU) richness, and using the diversity of higher taxa (such as family level) instead of OTU level represents a potential proxy for species-level diversity. IMPORTANCE Latitudinal gradients of forest soil fungal biodiversity in China have been previously investigated; however, the results of these studies were inconsistent. In the present study, I reanalyzed the data from these studies on all forest types in China and showed that the differences in forest soil fungal latitudinal diversity were caused by the different environments of continents and islands, as well as by the inconsistency between different classification standards. Accordingly, three suggestions were outlined for future studies on this and similar topics. This study makes a significant contribution to the literature because these findings can be used to improve our understanding of the forest soil fungal latitudinal diversity and as a basis for future studies.

Relationship between gut microbiota and nutritional status in patients on peritoneal dialysis

Malnutrition is a common complication in the dialysis population, both hemodialysis and peritoneal dialysis (PD). We report our exploratory study on the characteristics of intestinal microbiota and nutritional status in PD patients. The nutritional status of our PD patients were evaluated, and their feces were collected for 16S rRNA gene V3-V4 regions amplification and high-throughput sequencing. The characteristics and differences of microbiota between the well-nourished (W) and malnourished (M) groups were compared. We studied the genera and the operational taxonomic units (OTUs) within the genus of our patients, initially comparing the malnourished and the well- nourished groups and later on reanalyzing the whole group using these OTUs. At the OTU level, 6 bacteria were significantly correlated with the serum albumin level. The abundances of 2 OTUs (OTU208 Lachnospiraceae_incertae_sedi and OTU4 Bacteroides) were more in W group. Meanwhile, 4 OTUs (OTU225 Akkermansia, OTU87 Megasphaera, OTU31 Peptostreptococcaceae_incertae_sedi and OTU168 Clostridium_sensu_strictu) displayed higher abundance among individuals in M group. Notably, the OTU168 Clostridium_sensu_stricto was the only bacteria that significantly correlated with serum albumin (r = − 0.356, P = 0.05), pre-albumin (r = − 0.399, P = 0.02), and SGA (r = 0.458, P = 0.01). The higher the OTU168 Clostridium_sensu_strictu, the lower serum albumin and pre-albumin and a higher score of SGA signifying a worse nutritional status. Our preliminary findings suggested a relationship between the nutrition status and microbiota in PD patients. Our results provide a basis for further exploration of the interactions between malnutrition and intestinal flora in PD patients with potential interventions using probiotics and prebiotics.

Bacterial dynamics along the west coast of India during the non-monsoon and monsoon season

The West Coast of India (WCI) is influenced largely by semi-annual changes in the wind pattern and monsoonal currents. This is reported to cause upwelling which increases the phytoplankton growth in this region during the summer monsoon and it is recorded to be one of the world's highest primary productivity. Increase in the phytoplankton productivity is known to influence the microbial activity which is one of the key biogeochemical processes of the marine ecosystem as it plays an important role in the biotransformation of organic matter. However, the changes in the bacterial community structure and their heterotrophic enzyme activity with increasing primary production are not clearly understood from this region. Hence in this study, the bacterial dynamics along the WCI at Goa, Mangalore and Trivandrum, were investigated from the continental shelf, slope and off-shore region during the non-monsoon and monsoon season. Seasonal changes in the bacterial parameters such as abundance, viable counts and radioactivity based in-situ primary and bacterial productivity were estimated, along with the physicochemical characteristics. Statistical analysis shows a significant (p < 0.05) correlation between primary and bacterial productivity. Significant seasonal variations could also be established for the physicochemical parameters such as dissolved oxygen, nitrate, nitrite and phosphate, fluorescence values representing the chlorophyll concentration, bacterial abundance, viable counts and productivity. Taxonomic diversity studies on the cultivable bacterial morphotypes have shown that Proteobacteria, Firmicutes and Actinobacteria were the major phyla found during both the non-monsoon and monsoon season and Bacteroidetes, was represented only in the non-monsoon season. The bacterial community structure at phylum, genus and operational taxonomic unit levels also changed with higher diversity in the monsoon season. However, the hydrolytic enzyme activity of the bacterial morphotypes was comparatively lower during the monsoon season probably due to the active primary production. Though this study has improved our understanding of the monsoonal influence on the bacterial dynamics along the WCI, further studies based on metagenomic and transcriptome analysis are required to get a better understanding of the role played by the bacterial community from this region.