Differences In Microbial Abundance Research Articles

Analysis of pulmonary microecology and clinical characteristics of patients carrying human herpesvirus.

Aim: To investigate the impact of human herpes virus (HHV) carriage on lung microbiota, and its correlation with clinical features and laboratory indicators in patients.Methods: Retrospective analysis was conducted on 30 outpatient lung infection cases, which were divided into HHV (n=15) and non-HHV (n=15) groups. mNGS detected microbial composition. Microbial diversity and abundance were tested using Shannon and Chao1 indices. Their relationship with laboratory indicators were explored.Results: Significant differences in microbial abundance and distribution were found between two groups (p<0.05). Moreover, HHV group showed negative correlations (p<0.05) between Prevotella, Porphyromonas, Streptococcus and basophil/eosinophil percentages.Conclusion: HHV carriage impacts lung microbiota, emphasizing the need for clinicians to pay attention to HHV reactivation in outpatient lung infection patients.

Soil aggregate size distribution mediates microbial responses to prolonged acid deposition in a subtropical forest in south China

Extended exposure to acid rain has vastly limited soil microbial activity with the consequences for soil carbon (C) storage, but less is known about the microbial responses within soil aggregates that to some extent determine soil C stabilization. Here, we investigated the main microbial group compositions and the relevant potential enzyme activities within different soil aggregates sizes (microaggregates (<250 μm), small macroaggregates (250–2000 μm), and microaggregates (>2000 μm)) in a subtropical forest with decade-long simulated acid rain (SAR) treatments. Four SAR treatments were set by irrigating plots with water of different pH values (i.e., 3.0, 3.5, 4.0, and 4.5 as a control). Results showed that the SAR treatment significantly inhibited microbial activities, specifically decreasing both bacterial and fungal abundances, leading to declines in C-degrading potential enzyme activities. Conversely, potential enzyme activities related to phosphorus (P) and nitrogen (N) mineralization as well as the enzyme stoichiometry for P/N ratio significantly increased under the SAR treatment. The SAR treatment showed no significant differences in microbial abundance across the three soil aggregate sizes. However, it had a more pronounced effect on potential enzyme activities in their optimal aggregate sizes, such as hydrolytic enzymes like β-glucosidase in macroaggregates and oxidases like phenol oxidase and peroxidase in microaggregates. Overall, C-degrading potential enzyme activities were more strongly decreased in the microaggregates than in macroaggregates, and the distribution in aggregates was significantly altered, transforming from large to small sizes under the SAR treatment, which together may boost SOC stabilization and accumulation. Additionally, our findings indicate that prolonged acid rain also caused soil nutrient limitation and imbalance, particularly for P, in subtropical forests. This study highlights the importance of soil aggregate size in regulating microbial responses to acid rain, which should be integrated into ecosystem models to predict soil biogeochemical cycles under future climate conditions.

Effects and microbiota changes following oral lyophilized fecal microbiota transplantation in children with autism spectrum disorder.

Autism spectrum disorder (ASD) is a group of heterogeneous neurodevelopmental disorders that is characterized by core features in social communication impairment and restricted, repetitive sensory-motor behaviors. This study aimed to further investigate the utilization of fecal microbiota transplantation (FMT) in children with ASD, both with and without gastrointestinal (GI) symptoms, evaluate the effect of FMT and analyze the alterations in bacterial and fungal composition within the gut microbiota. A total of 38 children diagnosed with ASD participated in the study and underwent oral lyophilized FMT treatment. The dosage of the FMT treatment was determined based on a ratio of 1 g of donor stool per 1 kg of recipient body weight, with a frequency of once every 4 weeks for a total of 12 weeks. In addition, 30 healthy controls (HC) were included in the analysis. The clinical efficacy of FMT was evaluated, while the composition of fecal bacteria and fungi was determined using 16S rRNA and ITS gene sequencing methods. Median age of the 38 children with ASD was 7 years. Among these children, 84.2% (32 of 38) were boys and 81.6% (31 of 38) exhibited GI symptoms, with indigestion, constipation and diarrhea being the most common symptoms. Sample collections and assessments were conducted at baseline (week 0), post-treatment (week 12) and follow-up (week 20). At the end of the follow-up phase after FMT treatment, the autism behavior checklist (ABC) scores decreased by 23% from baseline, and there was a 10% reduction in scores on the childhood autism rating scale (CARS), a 6% reduction in scores on the social responsiveness scale (SRS) and a 10% reduction in scores on the sleep disturbance scale for children (SDSC). In addition, short-term adverse events observed included vomiting and fever in 2 participants, which were self-limiting and resolved within 24 h, and no long-term adverse events were observed. Although there was no significant difference in alpha and beta diversity in children with ASD before and after FMT therapy, the FMT treatment resulted in alterations in the relative abundances of various bacterial and fungal genera in the samples of ASD patients. Comparisons between children with ASD and healthy controls (HC) revealed statistically significant differences in microbial abundance before and after FMT. Blautia, Sellimonas, Saccharomycopsis and Cystobasidium were more abundant in children with ASD than in HC, while Dorea were less abundant. After FMT treatment, levels of Blautia, Sellimonas, Saccharomycopsis and Cystobasidium decreased, while levels of Dorea increased. Moreover, the increased abundances of Fusicatenibacter, Erysipelotrichaceae_UCG-003, Saccharomyces, Rhodotorula, Cutaneotrichosporon and Zygosaccharomyces were negatively correlated with the scores of ASD core symptoms. Oral lyophilized FMT could improve GI and ASD related symptoms, as well as sleep disturbances, and alter the gut bacterial and fungal microbiota composition in children with ASD. Chinese Clinical Trial Registry, ChiCTR2200055943. Registered 28 January 2022, www.chictr.org.cn.

Analysis of environmental biological effects and OBT accumulation potential of microalgae in freshwater systems exposed to tritium pollution

The ecological risk of tritiated wastewater into the environment has attracted much attention. Assessing the ecological risk of tritium-containing pollution is crucial by studying low-activity tritium exposure's environmental and biological effects on freshwater micro-environment and the enrichment potential of organically bound tritium (OBT) in microalgae and aquatic plants. The impact of tritium-contaminated wastewater on the microenvironment of freshwater systems was analyzed using microcosm experiments to simulate tritium pollution in freshwater systems. Low activity tritium pollution (105 Bq/L) induced differences in microbial abundance, with Proteobacteria, Bacteroidota, and Desulfobacterota occupying important ecological niches in the water system. Low activity tritium (105–107 Bq/L) did not affect the growth of microalgae and aquatic plants, but OBT was significantly enriched in microalgae and two aquatic plants (Pistia stratiotes, Spirodela polyrrhiza), with the enrichment coefficients of 2.08–3.39 and 1.71–2.13, respectively. At the transcriptional level, low-activity tritium (105 Bq/L) has the risk of interfering with gene expression in aquatic plants. Four dominant cyanobacterial strains (Leptolyngbya sp., Synechococcus elongatus, Nostoc sp., and Anabaena sp.) were isolated and demonstrated good environmental adaptability to tritium pollution. Environmental factors can modify the tritium accumulation potential in cyanobacteria and microalgae, theoretically enhancing food chain transfer.

Antibiotic resistance profiles of gut microbiota across various primate species in Guangxi.

Understanding the gut microbiota and antibiotic resistance gene (ARG) profiles in non-human primates (NHPs) is crucial for evaluating their potential impact on human health and the environment. In this study, we performed metagenomic analysis of 203 primate fecal samples, including nine NHP species and humans, to comprehensively characterize their gut microbiota and ARGs. Our study reveals the prevailing phyla in primates as Firmicutes, Bacteroidetes, Euryarchaeota, and Proteobacteria. The captive NHPs exhibited higher ARG abundance compared to their wild counterparts, with tetracycline and beta-lactam resistance genes prevailing. Notably, ARG subtypes in Trachypithecus leucocephalus (T. leucocephalus) residing in karst limestone habitats displayed a more dispersed distribution compared to other species. Interestingly, ARG profiles of NHPs clustered based on geographic location and captivity status. Co-occurrence network analysis revealed intricate correlations between ARG subtypes and bacterial taxa. Procrustes analysis unveiled a significant correlation between ARGs and microbial phylogenetic community structure. Taxonomic composition analysis further highlighted differences in microbial abundance among NHPs and humans. Our study underscores the impact of lifestyle and geographical location on NHP gut microbiota and ARGs, providing essential insights into the potential risks posed by NHPs to antibiotic resistance dissemination. This comprehensive analysis enhances our understanding of the interplay between NHPs and the gut resistome, offering a critical reference for future research on antibiotic resistance and host-microbe interactions.

Alterations in urinary microbiota composition in urolithiasis patients: insights from 16S rRNA gene sequencing.

To investigate the urinary microbiota composition in urolithiasis patients compared to healthy controls and to identify potential microbial markers and their association with clinical parameters. A total of 66 samples, comprising 45 from urolithiasis patients and 21 from healthy controls, were analyzed. 16S rRNA gene sequencing was employed to determine the microbiota composition. Various statistical and bioinformatics tools, including ANOVA, PCoA, and LEfSe, were utilized to analyze the sequencing data and identify significant differences in microbial abundance. No significant demographic differences were observed between the two groups. Post-quality control, clean tags ranged from 60,979 to 68,736. Significant differences in α-diversity were observed between the two groups. β-diversity analysis revealed distinct clustering of the urinary microbiota in urolithiasis patients and controls. Notably, Ruminococcaceae was predominant in urolithiasis samples, while Proteobacteria was more prevalent in healthy samples. Lactobacillus was significantly overrepresented in samples from healthy females. The urinary microbiota composition in urolithiasis patients is distinct from that of healthy controls. Specific microbial taxa, such as Ruminococcaceae and Proteobacteria, could serve as potential biomarkers for urolithiasis. The findings pave the way for further exploration of the role of microbiota in urolithiasis and the development of microbiome-based therapeutic strategies.

Characterization of disease-associated microbiota in hepatocellular carcinoma.

This study aimed to investigate the differences in the composition of microbial communities and related functions in hepatocellular carcinoma (HCC) tumours and matched normal tissues were investigated. Tumour tissues and matched normal samples were collected from 30 HCC patients. Genomic DNA was collected and subjected to sequencing of the V3 + V4 region of the 16S rRNA gene. The microbial community profiles and metabolic pathway predictions of the different groups were characterized and compared. Tumour and adjacent tissues had similar microbiota compositions but differed in abundance. Proteobacteria and Firmicutes abundance decreased and Cyanobacteria and Acidobacteria abundance increased in the tumour tissue. The microbial community diversity was higher in the tumour tissues than in adjacent samples, with potentially more dominant taxa in the adjacent tissues, including Firmicutes, Proteobacteria, and Actinobacteria. Acidobacteria, Cyanobacteria, and Chloroflexi were the dominant microbes in tumour tissues. A total of 46 metabolic pathways were identified. Global and overview maps were the most abundant pathways, followed by carbohydrate metabolism, energy metabolism, metabolism of cofactors and vitamins, and membrane transport. The top 50 most highly correlated microbial genera included Klebsiella, Rhodococcus, Ochrobactrum, and Azoarcus. Fonticella, Haloimpatiens, Brevibacterium, and Acidothermus were positively correlated with other microbial genera. The microbiota of adjacent tissues was more robust in the network analysis. This study revealed differences in microbial composition between HCC tumour tissues and normal tissues and differences in microbial abundance associated with different metabolic functions. Cyanobacteria, Proteobacteria, and Actinobacteria may play important roles in HCC.

Oral microbial communities in 5-year-old children with versus without dental caries

BackgroundCaries in young children has received more and more attention. The study of the oral microbiota may help to understand the polymicrobial etiology of dental caries.ObjectivesTo investigate the diversity and structure of microbial communities in saliva samples from 5-year-old children with versus without dental caries.MethodsA total of 36 saliva samples were collected from 18 children with high caries (HB group) and from 18 children without caries (NB group). Then, 16S rDNA was amplified from bacterial samples using polymerase chain reaction, and high-throughput sequencing was performed using Illumina Novaseq platforms.ResultsSequences were clustered into operational taxonomic units (OTUs), which were distributed among 16 phyla, 26 classes, 56 orders, 93 families, 173 genera, and 218 species. Firmicutes, Bacteroides, Proteobacteria, Actinobacteria, Fusobacteria, Patescibacteria, Epsilonbacteraeota, Cyanobacteria, Acidobacteria and Spirochaetes were basically the same in different groups, but their relative abundances were different. The core microbiome was defined as the species from 218 shared microbial taxa. The alpha diversity test showed that there were no significant differences in microbial abundance and diversity between the high caries and no caries groups. The results from principal coordinate analysis (PCoA) and hierarchical clustering showed that the two groups had similar microorganisms. The biomarkers of different groups were defined by LEfSe analysis to identify potential caries-related and health-related bacteria. Co-occurrence network analysis of dominant genera showed that oral microbial communities in the no caries group were more complex and aggregated than those in the high caries group. Finally, the PICRUSt algorithm was used to predict the function of the microbial communities from saliva samples. The obtained results showed that mineral absorption was greater in the no caries group than in the high caries group. BugBase was used to determine phenotypes present in microbial community samples. The obtained results showed that Streptococcus was greater in the high caries group than in the no caries group.ConclusionFindings of this study provide a comprehensive understanding of the microbiological etiology of dental caries in 5-year-old children and are expected to provide new methods for its prevention and treatment.

An in vitro model of the chicken gastrointestinal tract with special emphasis to the cecal microbiota

An in vitro model of the upper gastrointestinal tract as well as the chicken cecum was developed to have a predictive tool for estimating the production performance of animals by analyzing the feeding value of a certain diet. The upper gastrointestinal tract consists of a batch type model, whereas the cecal model is comprised of 4 semi-continuous connected vessels inoculated with cecal or fecal microbes. The upper gastrointestinal tract and cecal simulations were both run with a corn- and a wheat-based diet to simulate 2 typical feed types. Samples were collected after the 5-h cecal simulations and aliquots were frozen to assess inoculum stability. The microbiota was analyzed by 16S rRNA gene sequencing, whereas short chain fatty acids as microbial metabolites were analyzed by using gas chromatography. As expected, some significant differences in microbial abundance after simulation between the cecal and fecal slurry samples (P=0.001) were detected, as well between the fresh and frozen status (P=0.001), hence simulations inoculated with cecal and fresh samples being more diverse. For the measured metabolites, almost all of them increased (P < 0.05) significantly when comparing fresh and frozen inoculum. The present chicken intestinal in vitro model represents a rapid systematic screening system for studying dietary related microbial changes and reducing the need of animal sacrifice for experimentation.

Serum Levels of IFABP2 and Differences in Lactobacillus and Porphyromonas gingivalis Abundance on Gut Microbiota Are Associated with Poor Therapeutic Response in Rheumatoid Arthritis: A Pilot Study.

Intestinal dysbiosis is related to the physiopathology and clinical manifestation of rheumatoid arthritis (RA) and the response to pharmacologic treatment. The objectives of this study were (1) to analyze the effect of conventional synthetic disease modifying anti-rheumatic drugs (csDMARDs) on the abundance of gut microbiota's bacteria; (2) to evaluate the relationship between the differences in microbial abundance with the serum levels of intestinal fatty-acid binding protein 2 (IFABP2), cytokines, and the response phenotype to csDMARDs therapy in RA. A cross-sectional study was conducted on 23 women diagnosed with RA. The abundance of bacteria in gut microbiota was determined with qPCR. The ELISA technique determined serum levels of IFABP2, TNF-α, IL-10, and IL-17A. We found that the accumulated dose of methotrexate or prednisone is negatively associated with the abundance of Lactobacillus but positively associated with the abundance of Bacteroides fragilis. The Lactobacillus/Porphyromonas gingivalis ratio was associated with the Disease Activity Score-28 for RA with Erythrocyte Sedimentation Rate (DAS28-ESR) (r = 0.778, p = 0.030) and with the levels of IL-17A (r = 0.785, p = 0.027) in the group treated with csDMARD. Moreover, a relation between the serum levels of IFABP2 and TNF-α (r = 0.593, p = 0.035) was observed in the group treated with csDMARD. The serum levels of IFABP2 were higher in patients with secondary non-response to csDMARDs therapy. In conclusion, our results suggest that the ratios of gut microbiota's bacteria and intestinal permeability seems to establish the preamble for therapeutic secondary non-response in RA.

Microbial composition of egg component and its association with hatchability of laying hens.

The internal quality of eggs is critical for human consumption and embryonic development. However, microorganisms inside eggs have not been thoroughly investigated for their roles in determining the egg's internal quality. Here, a total of 21 hens were selected from more than 1,000 chickens based on their hatching results and were divided into high- and low-hatchability groups. Then, we collected 72 eggs from these 21 hens to obtain egg whites and yolks, including 54 fresh eggs and 18 eggs after 12 days of incubation. We characterized the microbial composition of egg yolks and whites, the microbial change along incubation, and differences in microbial abundance between the high- and low-hatchability groups. The results indicated that egg whites are not sterile. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the dominant phyla in egg yolk and white. There was a large difference in the microbial composition between egg whites and yolks, and this difference increased after 12 days of incubation. Egg whites have lower microbial diversity than egg yolks owing to the presence of antibacterial substances such as lysozyme in the egg white. After a 12-day incubation, the microbial diversity decreased in egg whites but increased slightly in egg yolks. Meanwhile, the microbes in egg white can migrate to egg yolk during incubation. Additionally, Genus Muribaculaceae was identified as a biomarker in egg yolks incubated for 12 days and was more often detected in healthy groups. On the contrary, more genus Rothia were found in the fresh egg yolk of the low hatchability groups and was considered to have low virulence. These findings shed light on the composition and differences in microbiota between egg yolks and whites and may open new avenues for studying embryonic development in chickens.

Chemical Links Between Redox Conditions and Estimated Community Proteomes from 16S rRNA and Reference Protein Sequences.

Environmental influences on community structure are often assessed through multivariate analyses in order to relate microbial abundances to separately measured physicochemical variables. However, genes and proteins are themselves chemical entities; in combination with genome databases, differences in microbial abundances directly encode for chemical variability. We predicted that the carbon oxidation state of estimated community proteomes, obtained by combining taxonomic abundances from published 16S rRNA gene sequencing datasets with reference microbial proteomes from the NCBI Reference Sequence (RefSeq) database, would reflect environmental oxidation-reduction conditions. Analysis of multiple datasets confirms the geobiochemical predictions for environmental redox gradients in hydrothermal systems, stratified lakes and marine environments, and shale gas wells. The geobiochemical signal is largest for the steep redox gradients associated with hydrothermal systems and between injected water and produced fluids from shale gas wells, demonstrating that microbial community composition can be a chemical proxy for environmental redox gradients. Although estimates of oxidation state from 16S amplicon and metagenomic sequences are correlated, the 16S-based estimates show stronger associations with redox gradients in some environments.

Comparison of Cecal Microbiota and Performance Indices Between Lean-Type and Fatty-Type Pekin Ducks.

Fatty-type (FT) Pekin ducks exhibit higher lipid deposition than lean-type (LT) ducks. The gut microbiota plays an important role in modulating fat metabolism. We compared the growth performance, slaughter performance, and cecal microbiota of FT and LT Pekin ducks and analyzed the role of cecal microbiota in lipid deposition in Pekin ducks. A total of 140 1-day-old FT and LT Pekin ducks with similar body weights were randomly assigned to 10 cages, with 14 ducks in each replicate. All ducks were fed commercial diets from 28 to 42 days of age. Results showed that the average body weight and feed intake of FT ducks were higher than those of LT ducks. The breast muscle and eviscerated percentages of LT ducks were higher than those of FT ducks; the abdominal fat and sebum percentages of LT ducks were lower than those of FT ducks at 6 weeks of age (P < 0.01). 16S DNA sequencing of the cecal microbiota revealed that the bacterial abundance differed between FT and LT ducks at 4 and 6 weeks of age. The abundance of Firmicutes was higher, while that of Fusobacteria and Fusobacterium was lower in LT ducks than in FT ducks at 4 weeks of age. The abundance of Spirochaetes was higher, while that of Firmicutes and Bacteroides was lower in LT ducks than in FT ducks at 6 weeks of age. The abundance of Spirochaetes and Brachyspira in LT ducks was higher at 6 weeks than at 4 weeks of age. Interestingly, the abundance of Firmicutes and Bacteroides in FT ducks was higher at 6 weeks of age than at 4 weeks of age, while that of Fusobacteria and Fusobacterium was lower at 6 weeks than at 4 weeks of age. Linear discriminant analysis effect size analysis showed that Spirochaetes, Brachyspira, Alistipes, Campylobacter, Megamonas, Butyricicoccus, and Fusobacteria may be involved in the fat metabolism pathway as specific markers. We reveal the differences in microbial abundance in the cecal microbiota between FT and LT Pekin ducks and provide an insight into the role of cecal microbiota in lipid deposition in Pekin ducks.

Differences Between Microbial Communities of Pinus Species Having Differing Level of Resistance to the Pine Wood Nematode.

The pine wood nematode (PWN), Bursaphelenchus xylophilus, is a destructive invasive species that exerts devastating effects on most native pines in invaded regions, while many of the non-native pines have resistance to PWN. Recently, increasingly more research is focused on how microbial communities can improve host resistance against pathogens. However, the relationship between the microbial community structures and varying levels of pathogen resistance observed in different pine tree species remains unclear. Here, the bacterial and fungal communities of introduced resistant pines Pinus elliottii, P. caribaea, and P. taeda and native susceptible pines healthy and wilted P. massoniana infected by PWN were analyzed. The results showed that 6057 bacterial and 3931 fungal OTUs were annotated. The pine samples shared 944 bacterial OTUs primarily in the phyla Proteobacteria, Acidobacteria, Firmicutes, Bacteroidetes, and Chloroflexi and 111 fungal OTUs primarily in phyla Ascomycota and Basidiomycota, though different pines had unique OTUs. There were significant differences in microbial community diversity between different pines, especially between the bacterial communities of resistant and susceptible pines, and fungal communities between healthy pines (resistant pines included) and the wilted P. massoniana. Resistant pines had a greater abundance of bacteria in the genera Acidothermus (class unidentified_Actinobacteria) and Prevotellaceae (class Alphaproteobacteria), but a lower abundance of Erwinia (class Gammaproteobacteria). Healthy pines had a higher fungal abundance of Cladosporium (class Dothideomycetes) and class Eurotiomycetes, but a lower abundance of Graphilbum, Sporothrix, Geosmithia (class Sordariomycetes), and Cryptoporus (classes Agaricomycetes and Saccharomycetes). These differences in microbial abundance between resistant and healthy pines might be associated with pathogen resistance of the pines, and the results of this study contribute to the studies exploring microbial-based control of PWN.

Association of Microbiome with Oral Squamous Cell Carcinoma: A Systematic Review of the Metagenomic Studies.

The past decade has witnessed a surge in epidemiological studies that have explored the relationship between the oral microbiome and oral cancer. Owing to the diversity of the published data, a comprehensive systematic overview of the currently available evidence is critical. This review summarises the current evidence on the metagenomic studies on the oral microbiome in oral cancer. A systematic search was conducted in Medline and Embase databases to identify original studies examining the differences in the oral microbiome of oral cancer cases and controls. A total of twenty-six studies were identified that reported differences in microbial abundance between oral squamous cell carcinoma (OSCC) and controls. Although almost all the studies identified microbial dysbiosis to be associated with oral cancer, the detailed qualitative analysis did not reveal the presence/abundance of any individual bacteria or a consortium to be consistently enriched in OSCC samples across the studies. Interestingly, few studies reported a surge of periodontopathogenic taxa, especially Fusobacteria, whereas others demonstrated a depletion of commensal taxa Streptococci. Considerable heterogeneity could be identified in the parameters used for designing the studies as well as reporting the microbial data. If microbiome data needs to be translated in the future, to complement the clinical parameters for diagnosis and prognosis of oral cancer, further studies with the integration of clinical variables, adequate statistical power, reproducible methods, and models are required.

324 Milk Fat Globule Membrane from Bovine Milk on Brain Development of Early Life

Abstract The milk fat globule membrane (MFGM) is instrumental for the fat delivery system into human and bovine milk, but is typically removed during the manufacture of infant formula. MFGM contains components that may impact neurodevelopment, including sialic acid, gangliosides, sphingomyelin, choline, glycerophospholipids, proteins, and cholesterol. This presentation will review the clinical trial evidence linking MFGM supplementation to beneficial outcomes in infants and will describe potential mechanistic evidence linking MFGM with neurocognitive outcomes arising from preclinical studies in piglets. Infants fed formula supplemented with a MFGM (4% total protein) from 2 to 6 months of age had improved neurocognitive development at 1 year of age compared to infants fed standard formula. Infants fed formula with MFGM (5.0 g/L) and lactoferrin (0.6 g/L) for 1 year had an accelerated neurodevelopmental profile at 1 year and improved language subcategories at 18 months compared to infants fed a standard formula. To investigate potential mechanisms, piglets were fed a CONT formula or a TEST formula with MFGM and lactoferrin at the same concentrations from 2 to 31 days of age. Piglets underwent spatial T-maze testing to assess learning and memory, and magnetic resonance imaging to measure brain micro- and macrostructure. TEST piglets had lower radial and mean diffusivities in the internal capsule, suggesting greater myelination. The internal capsule contains motor and sensory projections from the cortex to corticospinal tract. Piglets on the CONT diet displayed shorter latency to choice in the T-maze compared to TEST piglets, potentially indicating anxiety-like behaviors or greater impulsivity. Aspects of the microbiome-gut-brain-axis (MGBA) were investigated to uncover potential mechanisms. TEST piglets had higher protein abundance of tyrosine hydroxylase and vasoactive intestinal peptide, longer villi and greater disaccharidase activity in the small intestine and differences in microbial abundances in the ascending colon and feces, suggesting potential modulation of the MGBA by MFGM.

Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment

We aimed to explore the effects of type-2 diabetes mellitus (T2DM) and hypoglycemic therapy on the salivary microbiome in periodontitis patients and identify the potential salivary micro-biomarker for the early warning of T2DM. Saliva samples were collected from healthy individuals (Health), periodontitis patients (P), T2DM patients, periodontitis patients with T2DM (DAP), and DAP patients treated with Metformin (Met). Samples were determined by16S rRNA gene sequencing. 29 phyla, 322 genera, and 333 species of salivary microbiome were annotated. Compared to the Health group, the P and DAP group showed a significantly higher diversity of saliva microbiota, while the T2DM and Met group had no significant difference in microbial abundance but showed a trend of increasing diversity. Other than well-known periodontitis-inducing pathogens, the proportion of Prevotella copri, Alloprevotella rava, and Ralstonia pickettii, etc. were also significantly increased in periodontitis patients with or without T2DM. After effective glycemic control, the abundance of Prevotella copri, Alloprevotella rava, Ralstonia pickettii, etc. decreased in periodontitis patients with companion T2DM. The accuracies of the classification models in differentiating Health-vs.-P, DAP-vs.-P, and T2DM-vs.-P were 100%, 96.3%, and 98.1%, respectively. Hypoglycemic therapy could reconstruct the saliva microbiota and hence improve the localized conditions of diabetes patients with periodontitis.

Linking plant litter microbial diversity to microhabitat conditions, environmental gradients and litter mass loss: Insights from a European study using standard litter bags

Plant litter decomposition is a key process for carbon dynamics and nutrient cycling in terrestrial ecosystems. The interaction between litter properties, climatic conditions and soil attributes, influences the activity of microorganisms responsible for litter mineralization. So far, studies using standardized litters to investigate the response of bacterial and fungal communities under different environmental conditions are scarce, especially along wide geographic ranges.We used a standardized protocol to investigate the diversity of bacteria and fungi in plant litter with the aim of: (i) comparing the microbial communities of native and exotic litters with the community of local soil along a European transect from northern Finland to southern Italy, (ii) defining whether and to what extent, litter types with different traits represent selective substrates for microbial communities, (iii) disentangling the abiotic drivers of microbial diversity, and (iv) correlating the microbial diversity and species co-occurrences patterns with litter mass loss.We buried native litter and three exotic standardized litters (Deschampsia cespitosa, rooibos tea and green tea) at 12 European study sites. We determined litter mass loss after 94 days. We used an automated molecular DNA-based fingerprinting (ARISA) to profile the bacterial and fungal communities of each litter type and soil (180 samples in total).Microbial communities in native and exotic litters differed from local soil assemblages. Green tea and D. cespitosa litter represented more selective substrates compared to native litter and rooibos. Soil moisture and soil temperature were the major drivers of microbial community structure at larger scales, though with varying patterns according to litter type. Soil attributes (i.e. moisture and C/N ratios) better explained the differences in microbial abundances than litter type. Green tea degraded faster than all other litter types and accounted for the largest number of positive co-occurrences among microbial taxa. Litter mass loss was positively correlated with fungal evenness and with the percentage of positive co-occurrences between fungi.Our findings suggest that the microbial community at larger scales reflects the complex interplay between litter type and soil attributes, with the latter exerting a major influence. Mass loss patterns are in part determined by inter- and intra-kingdom interactions and fungal diversity.

Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine

BackgroundThe upper gastrointestinal tract plays a prominent role in human physiology as the primary site for enzymatic digestion and nutrient absorption, immune sampling, and drug uptake. Alterations to the small intestine microbiome have been implicated in various human diseases, such as non-alcoholic steatohepatitis and inflammatory bowel conditions. Yet, the physiological and functional roles of the small intestine microbiota in humans remain poorly characterized because of the complexities associated with its sampling. Rodent models are used extensively in microbiome research and enable the spatial, temporal, compositional, and functional interrogation of the gastrointestinal microbiota and its effects on the host physiology and disease phenotype. Classical, culture-based studies have documented that fecal microbial self-reinoculation (via coprophagy) affects the composition and abundance of microbes in the murine proximal gastrointestinal tract. This pervasive self-reinoculation behavior could be a particularly relevant study factor when investigating small intestine microbiota. Modern microbiome studies either do not take self-reinoculation into account, or assume that approaches such as single housing mice or housing on wire mesh floors eliminate it. These assumptions have not been rigorously tested with modern tools. Here, we used quantitative 16S rRNA gene amplicon sequencing, quantitative microbial functional gene content inference, and metabolomic analyses of bile acids to evaluate the effects of self-reinoculation on microbial loads, composition, and function in the murine upper gastrointestinal tract.ResultsIn coprophagic mice, continuous self-exposure to the fecal flora had substantial quantitative and qualitative effects on the upper gastrointestinal microbiome. These differences in microbial abundance and community composition were associated with an altered profile of the small intestine bile acid pool, and, importantly, could not be inferred from analyzing large intestine or stool samples. Overall, the patterns observed in the small intestine of non-coprophagic mice (reduced total microbial load, low abundance of anaerobic microbiota, and bile acids predominantly in the conjugated form) resemble those typically seen in the human small intestine.ConclusionsFuture studies need to take self-reinoculation into account when using mouse models to evaluate gastrointestinal microbial colonization and function in relation to xenobiotic transformation and pharmacokinetics or in the context of physiological states and diseases linked to small intestine microbiome and to small intestine dysbiosis.4XA-zWEeGyrQSh45UEwNDtVideo abstract.

Passive and active ecological restoration strategies for abandoned farmland leads to shifts in potential soil nitrogen loss by denitrification and soil denitrifying microbes

AbstractEcological restorations of abandoned farmland have been performed in degraded ecosystems with the goal of increasing ecosystem sustainability. The environmental benefits of ecological restoration can at least be partially neutralized by enhanced nitrogen (N) loss and potential nitrous oxide (N2O) emissions via denitrification. However, few studies have focussed on comparative analysis of the contributions of ecological restoration strategies to soil denitrifying microbes, particularly in arid and semiarid degraded ecosystems, where N is often the limiting nutrient. In this study, artificial afforestation (artificial forest sites) and natural revegetation (grassland sites) of abandoned farmland have an enhanced effect on reducing potential denitrification rates (PDR) compared with farmland sites and orchard sites, leading to lower N losses and potential N2O emissions. Combined analyses indicated that the greatest differences in microbial abundance, species richness, and diversity were observed among different ecological restoration strategies. The abundance, richness, and diversities of denitrifying microbes (nirS, nirK, and nosZ genes) were decreased by natural revegetation and artificial afforestation, leading to attenuated denitrifying activity responsible for the reduced PDR. Notably, the abundance and diversity of denitrifying microbes were dominant variables that explained the changes in PDR (up to 0.96). Overall, our results contribute to a better understanding of the feedback of denitrifying microorganisms to ecological restoration strategies and how these microorganisms collaboratively contribute to N loss and potential N2O emissions in arid and semiarid degraded ecosystems.