WITHDRAWN: Evaluating the association between body weight and the intestinal microbiota of weaned piglets via 16S rRNA sequencing

An Integrated Approach to Skeletal Muscle Health in Aging

A decline in muscle mass and function represents one of the most problematic changes associated with aging, and has dramatic effects on autonomy and quality of life. Several factors contribute to the inexorable process of sarcopenia, such as mitochondrial and autophagy dysfunction, and the lack of regeneration capacity of satellite cells. The physiologic decline in muscle mass and in motoneuron functionality associated with aging is exacerbated by the sedentary lifestyle that accompanies elderly people. Regular physical activity is beneficial to most people, but the elderly need well-designed and carefully administered training programs that improve muscle mass and, consequently, both functional ability and quality of life. Aging also causes alteration in the gut microbiota composition associated with sarcopenia, and some advances in research have elucidated that interventions via the gut microbiota-muscle axis have the potential to ameliorate the sarcopenic phenotype. Several mechanisms are involved in vitamin D muscle atrophy protection, as demonstrated by the decreased muscular function related to vitamin D deficiency. Malnutrition, chronic inflammation, vitamin deficiencies, and an imbalance in the muscle-gut axis are just a few of the factors that can lead to sarcopenia. Supplementing the diet with antioxidants, polyunsaturated fatty acids, vitamins, probiotics, prebiotics, proteins, kefir, and short-chain fatty acids could be potential nutritional therapies against sarcopenia. Finally, a personalized integrated strategy to counteract sarcopenia and maintain the health of skeletal muscles is suggested in this review.

Effect of stocking density and age on physiological performance and dynamic gut bacterial and fungal communities in Langya hens

Background

The characterization of colonization and dynamic changes related to gut microorganisms might be vital, as it presents an opportunity to quantify the co-variation between stocking densities and gut microbiome of dynamic distribution. The objective of this study was to determine the stocking density on physiological performance and dynamic distribution of gut microbiome (including bacterial and fungal communities) of Langya laying hens in the two development stages.

Methods

A randomized design with 2 × 3 factorial controls consisting of two development stages (24, 43 weeks-old) with three different stocking densities was performed. Three different stocking densities were allocated to a total of 300 11-week-old Langya laying hens (450 cm²/bird, 675 cm²/bird, 900 cm²/bird). Three housing densities were accomplished by raising different chickens per cage with the same floor size. The dependent variables of stocking densities at each sampling point were; growth performance, organs index, egg quality and the changes of dynamic gut bacterial and fungal communities in the cecum.

Results

Results showed that the stocking density didn’t affect liver index, eggshell thickness, breaking shell strength and egg shape index. Hens from the highest stocking density had the lowest body weight, fallopian tube index, egg weight and yolk colour score. Except for the yolk colour score, the measurement changes caused by age followed the opposite pattern as stocking density. We observed a substantial rise in taxa linked with health threats when stocking density was increased, including Talaromyces, Oscillospiraceae_UCG-002, Oscillospira, and Dielma. The opposite was observed with Bacteroides, Bifidobacterium, Lachnoclostridium, Eisenbergiella, and Kurtzmaniella. Also, most taxa were linked to polymicrobial infection in clinical cases, especially species whose percentage declined as the hens aged, such as Terrisporobacter, Faecalicoccus, Dialister, Cylindrocarpon etc. Whereas Sellimonas, Mitsuokella, Eurotium, Wardomyces and Cephalotheca had the opposite trend.

Conclusion

We speculated that excessive high density drove the abundance of bacteria and fungi connected with health problems. Where the gut microecology gradually reach a mature and balance status with age. Overall, this study demonstrates gut microbiome ecological processes in Langya layers at various stocking densities and finds possible connections between stocking density, microbiome and production performance. Our study will contribute to new insights associating suitable density patterns and production performance in laying hens by harnessing such a relative microbiome.

Linking microbial mechanism with bioelectricity production in sludge matrix-fed microbial fuel cells: Freezing/thawing liquid versus fermentation liquor

This first-attempt study elucidated the microbial mechanism associated with bioelectricity output in microbial fuel cells (MFCs) fed with sludge matrices of freezing/thawing (F/T) liquid versus fermentation liquor, while a novel schematic elucidation for exploring cooperative interactions in anodic microbial consortia of MFCs supplied with such two feeds toward electrogenesis was put forward. Moreover, the F/T liquid cultivated main genera of Azospira, Povalibacter, Thauera, Terrimonas, Alicycliphilus, Dokdonella and Simplicispira for dual organics degradation and electrogenesis with power density of 0.152 mW/m² and electrogenesis efficiency of 1.152 kWh/kg COD, while the fermentation liquor fostered higher diversity and medium evenness with the enrichment of Phenylobacterium, Cellulomonas, Edaphobacter, Burkholderia, Clostridium, Sphingomonas, Leifsonia and Microbacterium in anodic biofilm and causing larger power density of 0.182 mW/m² and 1.418 kWh/kg COD-electrogenesis efficiency. Comparative analysis results indicated that the anodic fermentative bacteria exert considerable influence on concurrent organics degradation and electricity production through the synergistic interactions with exoelectrogens toward stable running of MFCs. Besides, the higher anodic microbial diversity, relatively middling community evenness and larger abundance of functional genes associated with electrogenesis together played contributive roles on more power generation through MFCs for treating WAS matrix. This study was conducive to bring about some new microbial mechanism understanding on maximizing bioenergy recovery via MFCs in future sludge management.

Insights into microbial interaction profiles contributing to volatile fatty acids production via acidogenic fermentation of waste activated sludge assisted by calcium oxide pretreatment

This first-attempted study illustrated the calcium oxide (CaO) agentia-pretreatment for prompting waste activated sludge (WAS) solubilization and enhancing volatile fatty acids (VFAs) bio-production through acidogenic fermentation. The 15-h CaO pretreatment was capable to produce a soluble chemical oxygen demand (SCOD) yield of ca. 153.17 mg COD/g VS and VFAs generation efficiency of 327.8 mg COD/g VS with adding dosage of 0.07 g/g TS. The relative frequencies corresponded to metabolic functions profiling were promoted obviously by CaO pretreatment and contributed to biosolid decomposition/VFAs production in sludge fermentation. Main genera of Azonexus, Arcobacter, Acinetobacter, Thauera, Petrimonas, Clostrium and Macellibacteroides cooperated synergically toward triggering concurrent VFAs generation/biosolid biodegradation. Finally, the CaO-pretreatment displayed positive merits in terms of sludge biosolid decomposition/recoverable resource harvest as compared with other alkali pretreatments. This study might shed lights on enriching intensification strategy for WAS management toward high-efficiency of recoverable resource harvest with lower cost.

Impact of Protein Intake in Older Adults with Sarcopenia and Obesity: A Gut Microbiota Perspective

The continuous population increase of older adults with metabolic diseases may contribute to increased prevalence of sarcopenia and obesity and requires advocacy of optimal nutrition treatments to combat their deleterious outcomes. Sarcopenic obesity, characterized by age-induced skeletal-muscle atrophy and increased adiposity, may accelerate functional decline and increase the risk of disability and mortality. In this review, we explore the influence of dietary protein on the gut microbiome and its impact on sarcopenia and obesity. Given the associations between red meat proteins and altered gut microbiota, a combination of plant and animal-based proteins are deemed favorable for gut microbiota eubiosis and muscle-protein synthesis. Additionally, high-protein diets with elevated essential amino-acid concentrations, alongside increased dietary fiber intake, may promote gut microbiota eubiosis, given the metabolic effects derived from short-chain fatty-acid and branched-chain fatty-acid production. In conclusion, a greater abundance of specific gut bacteria associated with increased satiation, protein synthesis, and overall metabolic health may be driven by protein and fiber consumption. This could counteract the development of sarcopenia and obesity and, therefore, represent a novel approach for dietary recommendations based on the gut microbiota profile. However, more human trials utilizing advanced metabolomic techniques to investigate the microbiome and its relationship with macronutrient intake, especially protein, are warranted.

Effect of Modified Xijiao Dihuang Decoction () on Intestinal Flora and Th17/Treg in Rats with Radiation Enteritis

OBJECTIVE

To observe the effect of Modified Xijiao Dihuang Decoction (, MXDD) on rats with radiation enteritis, and explore its action mechanism.

METHODS

Thirty female Sprague Dawley rats were divided into the control, model, dexamethasone (DXM), golden bifid (GB) and MXDD groups using random number table, 6 rats in each group. Except the control group, the other rats were developed into radiation enteritis model by exposing to a single ⁶⁰Co-γ ray at a dose of 11 Gy. The rats in the DXM, GB and MXDD groups were treated with DXM (1.425 mg/kg), GB (0.8 g/kg) and MXDD (36.0 g/kg) for 3 days, respectively. Body weight and diarrhea condition of rats were evaluated daily. On day 3, the feces of rats were collected for intestinal flora detection and the small intestinal tissues were also collected. Bacterial species annotation, alpha and beta diversities as well as composition of intestinal flora were detected and compared. The protein and mRNA expressions of interleukin 17 (IL-17), retinoid-related orphan nuclear receptor gamma t (ROR-γt) and forkhead/ winged helix transcription factor p3 (FoxP3) were determined by Western blot and polymerase chain reaction, respectively. The abundance and diversity of intestinal flora as well as the proportion at the phylum and genus levels were assayed by 16S rRNA metagenome sequencing. Correlation between intestinal flora and Th17/Treg was analyzed by heatmap method.

RESULTS

On day 1 to 3 after radiation, compared with the control group, the body weight in model group was decreased (P<0.05 or P<0.01). Compared with the model group, MXDD could alleviate weight loss and diarrhea caused by irradiation. At the phylum level, MXDD cause a significant increase in Firmicutes, and a decrease in Proteobacteria (P<0.05 or P<0.01). At the genus level, MXDD reduced the proportion of Escherichia Shigella (P<0.01). In addition, IL-17 and FoxP3 mRNA and protein expression levels were down-regulated and ROR-γt was up-regulated by MXDD treatment (P<0.05). Besides, Firmicutes and Lactobacillus were positively correlated with FoxP3 (r=0.73, 0.79, respectively; P<0.01), negatively correlated with IL-17 (r=0.66, 0.64, respectively; P<0.01 or P<0.05) and ROR-γt (r0.73, 0.81, respectively; P<0.01). Proteobacteria and Escherichia Shigella both had positive correlation with IL-17 (r 0.77, 0.57, respectively; P<0.01 or P<0.05 ) and ROR-γt (r=0.94, 0.79, respectively; P<0.01) and negative correlation with FoxP3 (r0.74, 0.65; P<0.01).

CONCLUSION

MXDD could improve the survival status of irradiated rats by regulating the richness, diversity and composition of intestinal flora, and restoring the balance of Th17/Treg.

Selection of microbial biomarkers with genetic algorithm and principal component analysis

Background

Principal components analysis (PCA) is often used to find characteristic patterns associated with certain diseases by reducing variable numbers before a predictive model is built, particularly when some variables are correlated. Usually, the first two or three components from PCA are used to determine whether individuals can be clustered into two classification groups based on pre-determined criteria: control and disease group. However, a combination of other components may exist which better distinguish diseased individuals from healthy controls. Genetic algorithms (GAs) can be useful and efficient for searching the best combination of variables to build a prediction model. This study aimed to develop a prediction model that combines PCA and a genetic algorithm (GA) for identifying sets of bacterial species associated with obesity and metabolic syndrome (Mets).

Results

The prediction models built using the combination of principal components (PCs) selected by GA were compared to the models built using the top PCs that explained the most variance in the sample and to models built with selected original variables. The advantages of combining PCA with GA were demonstrated.

Conclusions

The proposed algorithm overcomes the limitation of PCA for data analysis. It offers a new way to build prediction models that may improve the prediction accuracy. The variables included in the PCs that were selected by GA can be combined with flexibility for potential clinical applications. The algorithm can be useful for many biological studies where high dimensional data are collected with highly correlated variables.

Faecal microbiome sequences in relation to the egg-laying performance of hens using amplicon-based metagenomic association analysis

Exploring the composition and structure of the faecal microbial community improves the understanding of the role of the gut microbiota in the gastrointestinal function and the egg-laying performance of hens. Therefore, detection of hen-microbial interactions can explore a new breeding marker for the selection of egg production due to the important role of the gut microbiome in the host's metabolism and health. Recently, the gut microbiota has been recognised as a regulator of host performance, which has led to investigations of the productive effects of changes in the faecal microbiome in various animals. In the present study, a metagenomics analysis was applied to characterise the composition and structural diversity of faecal microbial communities under two selections of egg-laying performance, high (H, n = 30) and low (L, n = 30), using 16S rRNA-based metagenomic association analysis. The most abundant bacterial compositions were estimated based on the operational classification units among samples and between the groups from metagenomic data sets. The results indicated that Firmicutes phylum has higher significant (P < 0.01) in the H group than in the L group. In addition, higher relative abundance phyla of Bacteroides and Fusobacteria were estimated in the H group than the L group, contrasting the phyla of Actinobacteria, Cyanobacteria and Proteobacteria were more relative abundance in the L group. The families (Lactobacillus, Bifidobacterium, Acinetobacter, Flavobacteriaceae, Lachnoclostridum and Rhodococcus) were more abundant in the H group based on the comparison between the H and L groups. Meanwhile, three types of phyla (Proteobacteria, Actinobacteria and Cyanobacteria) and six families (Acinetobacter, Avibacterium, Clostridium, Corynebacterium, Helicobacter and Peptoclostridium) were more abundant in the L group (P < 0.01). Overall, the selection of genotypes has enriched a relationship between the gut microbiota and the egg-laying performance. These findings suggest that the faecal microbiomes of chickens with high egg-laying performance have more diverse activities than those of chickens with low egg-laying performance, which may be related to the metabolism and health of the host and egg production variation.

Unraveling interactive characteristics of microbial community associated with bioelectric energy production in sludge fermentation fluid-fed microbial fuel cells

This first-attempt study deciphered the interactive characteristics of anodophilic microbial community-associated bioelectricity production in waste activated sludge (WAS) fermentation fluid-fed microbial fuel cells (MFCs). A novel schematic elucidation for illustrating synergistic interactions in anodic microbial consortia towards electrogenesis was proposed. Moreover, the specific genera of Pseudomonas, Desulfovibrio, Phyllobacterium, Desulfuromonas, Chelatococcus and Aminivibrio were dominant in anodic biofilms, leading to an electrogenesis efficiency of 1.254 kWh/kg COD and peak power density of 0.182 W/m² (at feeding level of 1.20 g COD/L). It was apparently higher than those MFCs fed with glucose/acetate. The fermentative species contributed positively in reorganizing microbial community structure in anodic biofilms, positively relating to electrogenesis via interactions with exoeletrogens in MFCs. Finally, a more electrogenesis was positively associated to larger anodic microbial diversity, relatively medium anodic community evenness, together with higher abundance of functional genes related to electrogenesis in functional species in MFCs fed with WAS fermentation fluid.

Insights into microbial community profiles associated with electric energy production in microbial fuel cells fed with food waste hydrolysate

Insights of microbial community profiles associated with electric energy production in microbial fuel cells (MFCs) fed with food waste hydrolysate (FWH) were investigated in this study. High power density of 0.173 W/m² was obtained from FWH which was produced from food waste after the pretreatment with fungal mash at an influent COD concentration of 1.2 g/L. The main genera in the MFCs fed with FWH were found to be Rummeliibacillus, Burkholderia, Enterococcus and Clostridium in anodic biofilms, leading to an electrogenesis efficiency of 0.977 kWh/kg COD higher than those obtained in MFCs with single carbon source feed. The key members in the anodic community responsible for electrogenesis were conceptually identified with their metabolic interactions in MFCs fed with FWH. It appeared that the syntrophic cooperation of fermentative species with exoelectrogens played an essential role in the generation of electric energy via specific microbes in anodic biofilm. The power produced from FWH was positively associated with microbial diversity, intermediate community evenness and abundance of functional genes for bioelectrogenesis.

Metagenomic insights into the microbiota profiles and bioaugmentation mechanism of organics removal in coal gasification wastewater in an anaerobic/anoxic/oxic system by methanol

Coal gasification wastewater is a typical high phenol-containing, toxic and refractory industrial wastewater. Here, lab-scale anaerobic-anoxic-oxic system was employed to treat real coal gasification wastewater, and methanol was added to oxic tank as the co-substrate to enhance the removal of refractory organic pollutants. The results showed that the average COD removal in oxic effluent increased from 24.9% to 36.0% by adding methanol, the total phenols concentration decreased from 54.4 to 44.9 mg/L. GC-MS analysis revealed that contents of phenolic components and polycyclic aromatic hydrocarbons (PAHs) were decreased compared to the control and their degradation intermediates were observed. Microbial community revealed that methanol increased the abundance of phenolics and PAHs degraders such as Comamonas, Burkholderia and Sphingopyxis. Moreover, functional analysis revealed the relative abundance of functional genes associated with toluene, benzoate and PAHs degradation pathways was higher than that of control based on KEGG database.

Intestinal Microbiome-Metabolome Responses to Essential Oils in Piglets

This study investigated the effects of dietary essential oils (EOs) on intestinal microbial composition and metabolic profiles in weaned piglets. The piglets were fed the same basal diet supplemented with EOs (EO) or without EOs (Con) in the current study. The results showed that the body weight gain was significantly increased, while the diarrhea incidence was significantly reduced in the EO group. In addition, EOs could modify the intestinal microbial composition of weaned piglets. The relative abundances of some beneficial bacterial species such as Bacilli, Lactobacillales, Streptococcaceae, and Veillonellaceae were significantly increased in the EO group. Metabolomics analysis indicated that protein biosynthesis, amino acid metabolism, and lipid metabolism were enriched in the EO group. And correlation analysis demonstrated that some gut bacterial genera were highly correlated with altered gut microbiota-related metabolites. Taken together, this study indicated that dietary EOs not only altered microbial composition and function but modulated the microbial metabolic profiles in the colon, which might help us understand EOs' beneficial effects on intestinal health of weaned piglets.

Fecal Microbiota Transplantation in Gestating Sows and Neonatal Offspring Alters Lifetime Intestinal Microbiota and Growth in Offspring

Previous studies suggest a link between intestinal microbiota and porcine feed efficiency (FE). Therefore, we investigated whether fecal microbiota transplantation (FMT) in sows and/or neonatal offspring, using inocula derived from highly feed-efficient pigs, could improve offspring FE. Pregnant sows were assigned to control or FMT treatments and the subsequent offspring to control treatment, FMT once (at birth), or FMT four times (between birth and weaning). FMT altered sow fecal and colostrum microbiota compositions and resulted in lighter offspring body weight at 70 and 155 days of age when administered to sows and/or offspring. This was accompanied by FMT-associated changes within the offspring's intestinal microbiota, mostly in the ileum. These included transiently higher fecal bacterial diversity and load and numerous compositional differences at the phylum and genus levels (e.g., Spirochaetes and Bacteroidetes at high relative abundances and mostly members of Clostridia, respectively), as well as differences in the abundances of predicted bacterial pathways. In addition, intestinal morphology was negatively impacted, duodenal gene expression altered, and serum protein and cholesterol concentrations reduced due to FMT in sows and/or offspring. Taken together, the results suggest poorer absorptive capacity and intestinal health, most likely explaining the reduced body weight. An additive effect of FMT in sows and offspring also occurred for some parameters. Although these findings have negative implications for the practical use of the FMT regime used here for improving FE in pigs, they nonetheless demonstrate the enormous impact of early-life intestinal microbiota on the host phenotype. IMPORTANCE Here, for the first time, we investigate FMT as a novel strategy to modulate the porcine intestinal microbiota in an attempt to improve FE in pigs. However, reprogramming the maternal and/or offspring microbiome by using fecal transplants derived from highly feed-efficient pigs did not recapitulate the highly efficient phenotype in the offspring and, in fact, had detrimental effects on lifetime growth. Although these findings may not be wholly attributable to microbiota transplantation, as antibiotic and purgative were also part of the regime in sows, similar effects were also seen in offspring, in which these interventions were not used. Nonetheless, additional work is needed to unravel the effects of each component of the FMT regime and to provide additional mechanistic insights. This may lead to the development of an FMT procedure with practical applications for the improvement of FE in pigs, which could in turn improve the profitability of pig production.

Exploring a Possible Link between the Intestinal Microbiota and Feed Efficiency in Pigs

Feed efficiency (FE) is critical in pig production for both economic and environmental reasons. As the intestinal microbiota plays an important role in energy harvest, it is likely to influence FE. Therefore, our aim was to characterize the intestinal microbiota of pigs ranked as low, medium, and high residual feed intake ([RFI] a metric for FE), where genetic, nutritional, and management effects were minimized, to explore a possible link between the intestinal microbiota and FE. Eighty-one pigs were ranked according to RFI between weaning and day 126 postweaning, and 32 were selected as the extremes in RFI (12 low, 10 medium, and 10 high). Intestinal microbiota diversity, composition, and predicted functionality were assessed by 16S rRNA gene sequencing. Although no differences in microbial diversity were found, some RFI-associated compositional differences were revealed, principally among members of Firmicutes, predominantly in feces at slaughter (albeit mainly for low-abundance taxa). In particular, microbes associated with a leaner and healthier host (e.g., Christensenellaceae, Oscillibacter, and Cellulosilyticum) were enriched in low RFI (more feed-efficient) pigs. Differences were also observed in the ileum of low RFI pigs; most notably, Nocardiaceae (Rhodococcus) were less abundant. Predictive functional analysis suggested improved metabolic capabilities in these animals, especially within the ileal microbiota. Higher ileal isobutyric acid concentrations were also found in low RFI pigs. Overall, the differences observed within the intestinal microbiota of low RFI pigs compared with that of their high RFI counterparts, albeit relatively subtle, suggest a possible link between the intestinal microbiota and FE in pigs.IMPORTANCE This study is one of the first to show that differences in intestinal microbiota composition, albeit subtle, may partly explain improved feed efficiency (FE) in low residual feed intake (RFI) pigs. One of the main findings is that, although microbial diversity did not differ among animals of varying FE, specific intestinal microbes could potentially be linked with porcine FE. However, as the factors impacting FE are still not fully understood, intestinal microbiota composition may not be a major factor determining differences in FE. Nonetheless, this work has provided a potential set of microbial biomarkers for FE in pigs. Although culturability could be a limiting factor and intervention studies are required, these taxa could potentially be targeted in the future to manipulate the intestinal microbiome so as to improve FE in pigs. If successful, this has the potential to reduce both production costs and the environmental impact of pig production.