Unclassified Ruminococcaceae Research Articles

Progression of swine fecal microbiota during early stages of life and its association with performance: a longitudinal study

BackgroundIt is vital to understand healthy gut microbiota composition throughout early life stages when environments are changing, and immunity is developing. There are limited large-scale longitudinal studies classifying healthy succession of swine microbiota. The objectives of this study were to (a) determine the microbiota composition of fecal samples collected from piglets within a few days after birth until one-week post-weaning, and (b) investigate the associations of early fecal microbiota with pig growth performance in nursery and later growing stages. Fecal samples were collected from nine cohorts of 40 pigs (n = 360) from distinct farrowing sources in Ontario and Quebec, Canada at four timepoints from birth to one-week post-weaning, with pig body weight was recorded at each fecal sampling.ResultsMicrobiota was dominated by the phyla Firmicutes, Bacteroides and Proteobacteria. There were notable differences in genera abundance between pigs from different provinces and farming systems. Over the early life stage, the genera Bacteroides, Escherichia/Shigella, and Clostridium cluster XIVa were abundant preweaning, while Prevotella dominated post-weaning. Hierarchical clustering identified three major stages of microbiota development, each associated with distinct composition. Stage one occurs from birth to 7 days, stage two from 7 days after birth until weaning, and stage three from weaning to one-week post-weaning. Three enterotypes were identified in stage two that showed differences in growth before weaning, and in the grower production stage. Piglets with a microbiota enterotype characterized by higher abundance of Prevotella and unclassified Ruminococcaceae had lower growth performance in the pre-weaning stage, and the growing stage.ConclusionThese findings help identify the timing of microbiota shifts across early swine life which may be the optimal time for external intervention to shift the microbiota to a beneficial state. The project findings should help decrease antimicrobial use, increase animal welfare, and have positive economic impacts.

Antibiotic Cocktail Effects on Intestinal Microbial Community, Barrier Function, and Immune Function in Early Broiler Chickens.

This study investigated the effects of an antibiotic cocktail on intestinal microbial composition, mechanical barrier structure, and immune functions in early broilers. One-day-old healthy male broiler chicks were treated with a broad-spectrum antibiotic cocktail (ABX; neomycin, ampicillin, metronidazole, vancomycin, and kanamycin, 0.5 g/L each) or not in drinking water for 7 and 14 days, respectively. Sequencing of 16S rRNA revealed that ABX treatment significantly reduced relative Firmicutes, unclassified Lachnospiraceae, unclassified Oscillospiraceae, Ruminococcus torques, and unclassified Ruminococcaceae abundance in the cecum and relative Firmicutes, Lactobacillus and Baccillus abundance in the ileum, but significantly increased richness (Chao and ACE indices) and relative Enterococcus abundance in the ileum and cecum along with relatively enriched Bacteroidetes, Proteobacteria, Cyanobacteria, and Enterococcus levels in the ileum following ABX treatment for 14 days. ABX treatment for 14 days also significantly decreased intestinal weight and length, along with villus height (VH) and crypt depth (CD) of the small intestine, and remarkably increased serum LPS, TNF-α, IFN-γ, and IgG levels, as well as intestinal mucosa DAO and MPO activity. Moreover, prolonged use of ABX significantly downregulated occludin, ZO-1, and mucin 2 gene expression, along with goblet cell numbers in the ileum. Additionally, chickens given ABX for 14 days had lower acetic acid, butyric acid, and isobutyric acid content in the cecum than the chickens treated with ABX for 7 days and untreated chickens. Spearman correlation analysis found that those decreased potential beneficial bacteria were positively correlated with gut health-related indices, while those increased potential pathogenic strains were positively correlated with gut inflammation and gut injury-related parameters. Taken together, prolonged ABX application increased antibiotic-resistant species abundance, induced gut microbiota dysbiosis, delayed intestinal morphological development, disrupted intestinal barrier function, and perturbed immune response in early chickens. This study provides a reliable lower-bacteria chicken model for further investigation of the function of certain beneficial bacteria in the gut by fecal microbiota transplantation into germ-free or antibiotic-treated chickens.

Modulatory Effects of Lactarius hatsudake on Obesity and Gut Microbiota in High-Fat Diet-Fed C57BL/6 Mice.

Lactarius hatsudake (LH), a great wild endemic fungus, contains rich nutritional components with medicinal properties. The effects of LH on body weight, liver weight, liver injury, blood lipids, and gut microbiota in C57BL/6 mice fed a high-fat diet (HFD) for 8 weeks was examined in this research. Though there was no clear impact on weight loss, the findings indicate that LH treatment effectively decreased liver damage caused by HFD, as well as lowered serum total cholesterol, triacylglycerol, and low-density lipoprotein cholesterol levels. Additionally, it positively influenced gut microbiota to resemble that of mice on a normal diet. In HFD-fed mice, LH markedly boosted the levels of Parabacteroides, unclassified Muribaculaceae, Oscillibacter, and unclassified Oscillospiraceae, while reducing the abundance of Lachnospiraceae NK4A136 group and Erysipelatoclostridium, as well as the ratio of Firmicutes to Bacteroidetes. Further analysis of correlation indicate a possible connection between obesity and gut microbiota. Obesity-related indices show a positive association with unclassified Eubacterium coprostanoligenes group, Blautia, and Erysipelatoclostridium, while displaying a negative correlation with unclassified Muribaculaceae, unclassified Clostridia vadinBB60 group, Helicobacter, Oscillibacter, unclassified Ruminococcaceae, Parabacteroides, and unclassified Oscillospiraceae. The results suggest that LH can help combat obesity and may have the potential to be utilized as a functional food.

Effects of dietary mulberry leaves on growth, production performance, gut microbiota, and immunological parameters in poultry and livestock: a systematic review and meta-analysis.

This study aimed to assess the effects of dietary mulberry leaves on the growth, production performance, gut microbiota, and immunological parameters of poultry and livestock. The PubMed, Embase, and Scopus databases were systematically analyzed to identify pertinent studies up to December 2022. The effects of mulberry leaf diet was assessed using the weighted mean difference, and the 95% confidence interval was calculated using a random-effects model. In total, 18 studies that sampled 2,335 poultry and livestock were selected for analysis. Mulberry leaves improved the average daily gain and reduced the feed/meat ratio in finishing pigs, and the average daily gain and average daily feed intake in chicken. In production performance, mulberry leaves lowered the half carcass weight, slaughter rate, and loin eye area in pigs, and the slaughter rate in chickens. Regarding meat quality in pigs, mulberry leaves reduced the cooked meat percentage, shear force, crude protein, and crude ash, and increased the 24 h pH and water content. In chickens, it increased the drip loss, shear force, 45 min and 24 h pH, crude protein, and crude ash. Mulberry leaves also affect the abundances of gut microbiota, including Bacteroides, Prevotella, Megamonas, Escherichia-Shigella, Butyricicoccus, unclassified Ruminococcaceae, Bifidobacterium, Lactobacillus, and Escherichia coli in poultry and livestock. Mulberry leaves at different doses were associated with changes in antioxidant capacity in chickens, and immune organ indexes in pigs. With respect to egg quality, mulberry leaves at different doses improved the shell strength, yolk color, eggshell thickness, and eggshell weight. However, moderate doses diminished the egg yolk ratio and the egg yolk moisture content. In general, dietary mulberry leaves improved the growth, production performance, and immunological parameters in poultry and livestock, although the effects varied at different doses.

Sympathovagal quotient and resting-state functional connectivity of control networks are related to gut Ruminococcaceae abundance in healthy men

IntroductionHeart rate variability (HRV), brain resting-state functional connectivity (rsFC), and gut microbiota (GM) are three recognized indicators of health status, whose relationship has not been characterized. We aimed to identify the GM genera and families related to HRV and rsFC, the interaction effect of HRV and rsFC on GM taxa abundance, and the mediation effect of diet on these relationships. MethodsEighty-eight healthy, young Colombian men were included in this cross-sectional study. HRV metrics were extracted from 24-hour Holter monitoring data and the resting functional connectivity strength (FCS) of 15 networks were derived from functional magnetic resonance imaging. Gut microbiota composition was assessed using the sequences of the V3-V4 regions of the 16 S rRNA gene, and diet was evaluated using a food frequency questionnaire. Multivariate linear regression analyses were performed to evaluate the correlations between the independent variables (HRV metrics and FCS) and the dependent variables (GM taxa abundance or alpha diversity indexes). Mediation analyses were used to test the role of diet in the relationship between HRV and GM. ResultsThe sympathovagal quotient (SQ) and the FCS of control networks were positively correlated with the abundance of the gut Ruminococcaceae family and an unclassified Ruminococcaceae genus (Ruminococcaceae_unc). Additionally, the interaction between the FCS of the control network and SQ reduced the individual main effects on the Ruminococcaceae_unc abundance. Finally, reduced habitual fiber intake partially mediated the relationship between SQ and this genus. ConclusionTwo indicators of self-regulation, HRV and the rsFC of control networks, are related to the abundance of gut microbiota taxa in healthy men. However, only HRV is related to habitual dietary intake; thus, HRV could serve as a marker of food choice and GM composition in the future.

Effect of Artemisia absinthium (Asteraceae) and Cobalt Supplementation on Rumen Bacterial Community in Cattle

Background: One of the key tasks of livestock development is to reduce the amount of feed needed for raising and fattening cattle, as well as increase the efficiency of feed use. A possible solution to these problems are plant-based feed additives containing various phytochemical compounds, both individually and together with metallic trace elements, to improve the functioning of the gastrointestinal tract of animals. The aim of the study was to assess the effect on the microbiota of the cattle rumen of the vegetable feed components Artemisiae absinthil (bitter plant A. absinthium) and CoCl2 (cobalt II chloride). Methods: Study the effect of the herb Artemisia absinthium (A. absinthium) and CoCl2 (cobalt II chloride) on the microbiome of cattle rumen. The studies were conducted on a cannula animal model, Bos taurus (Kazakh white-headed cattle), after feeding an experimental feed additive, A. absinthium, either alone or in combination with CoCl2. The experiment was carried out in four repetitions using a 4 × 4 Latin square. Animals in the I experimental group were additionally given A. absinthium at a dose of 2.0 g/kg of dry matter (DM); in the II experimental group, A. absinthium at a dose of 2.0 g/kgDM with additional CoCl2 (1.5 mg/kgDM); and in the III experimental group, only CoCl2 (1.5 mg/kgDM). The contents of the scar were collected for further analysis, which was performed by high-performance sequencing (NGS) of 16S rRNA gene ampicons. Result: There was difference in the microbiome of the rumen of cattle between the control and experimental groups, both at the level of the phylum’s and at the genus level. The dominant phylum in all groups were Firmicutes and Bacteroidetes. A study of the microbiome of the rumen revealed groups of microorganisms capable of producing carbohydrate-active enzymes (CAZyms) and destroying structural hydrocarbons. In the group using A. absinthium, a symbiotic link was established for the genus Akkermansia and the unclassified Bacteroidales linear regression (R2 = 0.93, p = 0.0435) and for the unclassified Ruminococcaceae and the genus Akkermansia (R2 = 0.75, p = 0.05).

Postbiotics from Saccharomyces cerevisiae fermentation stabilize rumen solids microbiota and promote microbial network interactions and diversity of hub taxa during grain-based subacute ruminal acidosis (SARA) challenges in lactating dairy cows.

High-yielding dairy cows are commonly fed high-grain rations. However, this can cause subacute ruminal acidosis (SARA), a metabolic disorder in dairy cows that is usually accompanied by dysbiosis of the rumen microbiome. Postbiotics that contain functional metabolites provide a competitive niche for influential members of the rumen microbiome, may stabilize and promote their populations, and, therefore, may attenuate the adverse effects of SARA. This study used a total of 32 rumen-cannulated lactating dairy cows, which were randomly assigned into four treatments: no SCFP (control), 14 g/d Original XPC (SCFPa), 19 g/d NutriTek (SCFPb-1X), and 38 g/d NutriTek (SCFPb-2X) (Diamond V, Cedar Rapids, IA) from 4 weeks before until 12 weeks after parturition. Grain-based SARA challenges were conducted during week 5 (SARA1) and week 8 (SARA2) after parturition by replacing 20% dry matter of the base total mixed ration (TMR) with pellets containing 50% ground barley and 50% ground wheat. The DNA of rumen solids digesta was extracted and subjected to V3-V4 16S rRNA gene sequencing. The characteristics of rumen solids microbiota were compared between non-SARA (Pre-SARA1, week 4; Post-SARA1, week 7; and Post-SARA2, weeks 10 and 12) and SARA stages (SARA1/1, SARA1/2, SARA2/1, SARA2/2), as well as among treatments. Both SARA challenges reduced the richness and diversity of the microbiota and the relative abundances of the phylum Fibrobacteres. Supplementation with SCFP promoted the growth of several fibrolytic bacteria, including Lachnospiraceae UCG-009, Treponema, unclassified Lachnospiraceae, and unclassified Ruminococcaceae during the SARA challenges. These challenges also reduced the positive interactions and the numbers of hub taxa in the microbiota. The SCFPb treatment increased positive interactions among microbial members of the solids digesta and the number of hub taxa during the SARA and non-SARA stages. The SCFPb-2X treatment prevented changes in the network characteristics, including the number of components, clustering coefficient, modularity, positive edge percentage, and edge density of the microbiota during SARA challenges. These challenges reduced predicted carbohydrate and nitrogen metabolism in microbiota, whereas SCFP supplementation attenuated those reductions. Supplementation with SCFP, especially the SCFPb-2X attenuated the adverse effects of grain-based SARA on the diversity and predicted functionality of rumen solids microbiota.

In vitro fermentation of substrates from Saccharina latissima by broiler chicken’s caecal microbiota

This study investigated seasonal variations in the composition of the kelp species Saccharina latissima cultivated on the Swedish west coast and, using an in vitro fermentation system, evaluated the effect of fermented whole S. latissima biomass or biomass components on the gut microbiota of broiler chickens. Caecal contents of six Ross 308 broilers fed a standard wheat and soy-based diet were retrieved on two different occasions, with three birds sampled per occasion. Two in vitro fermentation batches (A, B) were established using caecal contents as inoculum, and whole S. latissima, ethanol-washed S. latissima, laminarin extract or inulin (control) as substrate. Total short-chain fatty acid (SCFA) content, gas production, pH and changes in microbiota composition were studied after 6, 12 and 24 h of fermentation. Analysis of seasonal variations revealed that S. latissima harvested in June had the highest laminarin content and lowest ash and crude protein content. Broiler microbiota, SCFA profile, gas production and pH mainly varied depending on fermentation inoculum, but there were also some variations depending on substrate. For instance, uncultured bacterium from Clostridiales_vadinBB60_group showed higher relative abundance (RA) in batch A, while Faecalibacterium showed higher RA in batch B. Whole and ethanol-washed S. latissima resulted in highest RA of unclassified Ruminococcaceae and Tyzzerella for both batches, while ethanol-washed S. latissima and laminarin gave highest RA of Erysipelatoclostridium. Inulin resulted in highest RA for the genus Subdoligranulum. Acetic, n-butyric and propionic acid were the main fermentation products and total SCFA level was higher in batch B. Within batch B, inulin and laminarin generated higher levels of acetic and butyric acid. When using inulin and laminarin, gas production was lower in batch B compared with batch A. In summary, this study showed that S. latissima is a good source of laminarin, especially when harvested in summer. Within the in vitro system, the microbiota was affected by different substrates, but inoculum source was identified as an important contributor to microbial community development during fermentation.

Metagenomics-Based Analysis of the Effect of Rice Straw Substitution for a Proportion of Whole-Plant Corn Silage on the Rumen Flora Structure and Carbohydrate-Active Enzymes (CAZymes)

The purpose of this study was to investigate the effects of replacing a portion of whole-plant corn silage with straw on the rumen microbial community structure and carbohydrate-active enzyme activity. The experiment employed a single-factor randomized trial design, with eight late-lactation Chinese Holstein dairy cows being randomly divided into two groups of four replicates each. The control group (CS group) was fed a diet consisting of alfalfa silage and a mixture of alfalfa and whole-plant corn silage, while the experimental group (RS group) received a diet in which one-third of the corn silage was replaced with straw while keeping the other components unchanged. The experiment lasted for a total of 21 days, with a pre-feeding period of 14 days and a formal period of 7 days. The rumen fluid collected on day 21 was used for the rumen fermentation parameters and metagenomic analysis. The concentrations of acetic acid, propionic acid, butyric acid, and total volatile fatty acids (TVFA) in the rumen of RS group cows were significantly lower than those in the CS group (p < 0.01). The ratio of acetic acid to propionic acid was significantly higher in the RS group compared to the CS group (p < 0.01). Metagenomic sequencing revealed that at the genus level, compared to the CS group, the abundance of unclassified bacteria, Bacteroides, Alistipes, Butyrivibrio, Chlamydia, Fibrobacter, unclassified Ruminococcaceae, and unclassified Bacteroidetes in the rumen of RS group cows increased, while the abundance of Eubacterium decreased ([LDA > 3.6], p < 0.05). Compared to the CS group, the enzymatic activities of α-L-arabinofuranosidase (EC3.2.1.55), β-xylosidase (EC3.2.1.37), β-glucosidase (EC3.2.1.21), β-glucosylceramidase (EC3.2.1.45), xylanase (EC3.2.1.8), and arabinanase (EC3.2.1.99) in the rumen of RS group cows increased (p < 0.05). According to the correlation analysis, Alistipes, Bacteroides, and Butyrivibrio showed a significant negative correlation with propionic acid (p < 0.05) and a significant positive correlation with the acetic acid-to-propionic acid ratio (p < 0.05). They also showed a significant positive correlation with GH2, GH3, GH20, GH29, GH43, GH78, GH92, CE1, GT4, β-glucosidase (EC3.2.1.21), α-L-arabinofuranosidase (EC 3.2.1.55), β-xylosidase (EC 3.2.1.37), β-glucosylceramidase (EC 3.2.1.45), xylanase (EC 3.2.1.8), and arabinanase (EC 3.2.1.99) (p < 0.05). In summary, straw can not only alter the composition and structure of the rumen microbiota in cows but also affect the relative abundance of CAZymes at different levels within the rumen. Cows may, thus, potentially improve the degradation efficiency of straw diets by increasing the abundance of certain rumen microbiota and enzymes.

Alfalfa intervention alters the colonization of rumen epithelial bacteria to promote rumen development and lamb health during early life

Understanding the rumen epithelial (RE) microbial community structure and population dynamics of young ruminant during development is fundamental in promoting the establishment of a well-developed rumen for animal health and production. In this study, 10-day-old Hu lambs were fed with milk replacer (B-10), milk replacer and starter (STA) or milk replacer and starter supplemented with alfalfa (S-ALF). The RE bacteria of lambs at d10, 17, 24, 38, 45 and 66 were assessed to characterize RE bacterial colonization during early life and its response to fiber intervention. In B-10 lambs, 434 operational taxonomic units (OTUs) belonging to 57 core genera were observed in the RE. A number of the fibrolytic bacteria (Butyrivibrio and unclassified Ruminococcaceae), the pectinolytic bacterium (Treponema), the protein and fat digester (p-75-a5), the short-chain fatty acids producers ([Eubacterium], Succiniclasticum, unclassified Succinivibrionaceae, and Clostridiales), and the non-fermentive bacterium (Mogibacterium) were induced by alfalfa intervention in the S-ALF group during preweaning period, which attributed to a more mature RE bacterial community. OTUs belonging to Butyrivibrio, Succiniclasticum, Bacteroidales, Desulfovibrio, Clostridiales, and Succiniclasticum induced by alfalfa intervention were positively correlated with rumen tissue genes involved in fatty acid metabolism, barrier function, and PI3K-Akt, FoxO, and calcium signaling pathways. During the postweaning period, the RE bacterial composition of STA group changed significantly, while the S-ALF group did not. Our results suggested that alfalfa induced changes in RE bacteria during preweaning period which was associated with rumen health. The findings provide guidance for improving rumen health by manipulating RE bacteria during early life.

Inulin has a beneficial effect by modulating the intestinal microbiome in a BALB/c mouse model.

Food allergy is an important health problem that affects human quality of life and socioeconomic development, and its treatment requires improvement. Intestinal flora dysbiosis is closely associated with food allergies. Asensitised mouse model was established by the intraperitoneal injection of ovalbumin (OVA). The mice were randomly divided into four groups: control, model, high-dose (H), and low-dose (L) inulin. The mice were administered water containing different concentrations of inulin four weeks before the OVA injection. Body weight changes were monitored. After the last OVA injection, the mice were scored for allergic reactions. The levels of total immunoglobulin E (IgE) and diamine oxidase (DAO) in the serum and secretory IgA (sIgA) in the small intestinal mucus were measured, and 16S rRNA sequencing of the faecal flora was performed to evaluate microbial parameters. The intestinal flora biomarkers, correlations between them, and biochemical indicators were analysed. Inulin treatment had no effect on the body weight of OVA-sensitised mice but attenuated allergic reactions and intestinal injury in mice. Compared with the control group, the model group had significantly higher levels of serum DAO and IgE and significantly lower levels of intestinal mucus IgA. IgA levels in the intestinal mucus of mice treated with inulin prior to OVA sensitisation were higher than those in non-inulin-treated OVA-sensitised mice. Furthermore, analysis of operational taxonomic units showed that inulin treatment decreased the abundance of Alloprevotella, Rikenellaceae RC9, Eubacterium siraeum, and Eubacterium xylanophilum, and increased the abundance of Blautia and Lachnospiraceae. Serum DAO levels were positively associated with Eubacterium siraeum, Alloprevotella, Eubacterium xylanophilum, and Odoribacter and negatively associated with Blautia, Tyzzerella, Alistipes, Desulfovibrionaceae, and Ruminococcaceae UCG005. In addition, IgE levels were positively associated with Eubacterium siraeum, Alloprevotella, Eubacterium xylanophilum, Odoribacter, and Citrobacter and negatively associated with Blautia, unclassified Ruminococcaceae, and Alistipes. IgA exhibited significant positive correlation with Blautia, norank_f_Eubacterium coprostanoligenes, Alistipes, norank Desulfovibrionaceae, Muribaculum, and Ruminococcaceae U C G 005 and significant negative correlation with Eubacterim siraeum, Eubacterium xylanophilum, Odoribacter, and Citrobacter. Inulin exerts a protective effect against food allergies in mice, which is partially mediated by alterations in the gut microbiota.

Changes in the Concentration of Amino Acids and Bacterial Community in the Rumen When Feeding Artemisia absinthium and Cobalt Chloride

The aim of the study was to analyze the effect of a plant feed additive based on Artemisia absinthium and the metal trace element CoCl2 (cobalt chloride II) on the metabolism of amino acids closely related to the energy of feed and the bacterial community of the rumen of Kazakh white-headed bulls. Animals were divided into four groups: (A)—the control group of animals received the basic diet (BD), (B)—animals of the experimental group I were additionally given A. absinthium at a dose of 2.0 g/kg of dry matter (DM), (C)—II experimental group A. absinthium at a dose of 2.0 g/kg DM with additional CoCl2 (1.5 mg/kg/DM), and (D)—III experimental group was given only CoCl2 (1.5 mg/kg/DM) to study the rumen metabolism of amino acids and bacterial diversity of animals, rumen cannula were installed, the experiment was carried out using a 4 × 4 Latin square. It was found that additional feeding of A. absinthium, both separately and in combination with CoCl2, led to a change in the indices of the alpha biodiversity of the bacterial community. Correlation analysis revealed a linear relationship between the concentration of amino acids and the rumen bacterial community (p ≤ 0.05). The relationship between the values of amino acid concentrations and certain OTUs was established, with a possible percentile probability of 95% for the genera unclassified Lachnospiraceae, unclassified Clostridiales, unclassified Bacteroidales, Fibrobacter, Ihubacter, Phocaeicola, Paludibacter, Akkermansia, Vampirovibrio, unclassified Ruminococcaceae, and Alistipes. Thus, the use of A. absinthium and CoCl2 as feed additives, both in combination and without, leads to a change in the taxonomic structure affecting the concentration of amino acids. However, further research is needed to better understand the effectiveness and safety of these supplements.

The Gut Microbiota Differ in Exclusively Breastfed and Formula-Fed United States Infants and are Associated with Growth Status

BackgroundEvidence regarding the effects of infant feeding type (exclusive breastfeeding compared with exclusive formula feeding) on the gut microbiota and how it impacts infant growth status is limited. ObjectivesThe primary objective was to compare gut microbiota by feeding type and characterize the associations between gut microbiota and infant growth status. MethodsStool samples from healthy, full-term infants (4–5 mo-old) who were either exclusively breastfed (BF) or exclusively formula-fed (FF) in Denver, CO, United States were collected, and fecal 16S ribosomal ribonucleic acid gene-based profiling was conducted. Length and weight were measured at the time of stool collection. Length-for-age z-score, weight-for-age z-scores (WAZ), and weight-for-length z-scores were calculated based on the World Health Organization standards. Associations between gut microbial taxa and anthropometric z-scores were assessed by Spearman’s rank correlation test. ResultsA total of 115 infants (BF n = 54; FF n = 61) were included in this study. Feeding type (BF compared with FF) was the most significant tested variable on gut microbiota composition (P < 1 × 10-⁶), followed by mode of delivery and race. Significant differences were observed in α-diversity, β-diversity, and relative abundances of individual taxa between BF and FF. BF infants had lower α-diversity than FF infants. Abundances of Bifidobacterium and Lactobacillus were greater in the breastfeeding group. FF infants had a higher relative abundance of unclassified Ruminococcaceae (P < 0.001), which was associated with a higher WAZ (P < 0.001) and length-for-age z-score (P < 0.01). Lactobacillus was inversely associated with WAZ (P < 0.05). ConclusionsFeeding type is the main driver of gut microbiota differences in young infants. The gut microbiota differences based on feeding type (exclusive breast- or formula feeding) were associated with observed differences in growth status.This trial was registered at clinicaltrials.gov as NCT02142647, NCT01693406, and NCT04137445.

The Effect of Dietary Synbiotics in Actively Racing Standardbred Horses Receiving Trimethoprim/Sulfadiazine.

Synbiotics are often provided to horses receiving antibiotics to protect against microbiome disturbances, despite a lack of evidence for efficacy. The purpose of this study was to evaluate the effect of a synbiotic product in horses receiving antibiotics. Sixteen actively racing Standardbred horses were randomly allocated (four-way crossover) to one of four groups: antibiotics (10 days; AB), synbiotics (28 days; PROBIOPlusTM; PBP), PBP + AB, or Control. The fecal microbiome was investigated using 16S rRNA sequencing, and fecal dry matter (DM; %), pH, and scores (FS; 0-9) were measured. Data were analyzed with two-way ANOVA. Results found microbiota differences in community membership between PBP + AB and all other treatments during and after antibiotic treatment. During antibiotic treatment, AB and PBP + AB were significantly different from Control. After antibiotic treatment, PBP + AB was significantly different from all other treatments. The few differences found in relative abundance of phyla or predominant genera were mostly in fiber degrading bacteria. The Fibrobacter population was significantly higher in AB and PBP + AB horses than Control. Unclassified Ruminococcaceae was significantly higher in Control than AB and PBP. After antibiotic treatment, PBP + AB horses were significantly higher than PBP horses. In conclusion, these data provide support for the ability of PROBIOPlus™ to maintain healthy gastrointestinal microbiome during antibiotic treatment.

Effects of Fumarate and Nitroglycerin on In Vitro Rumen Fermentation, Methane and Hydrogen Production, and on Microbiota.

This study aimed to investigate the effects of fumarate and nitroglycerin on rumen fermentation, methane and hydrogen production, and microbiota. In vitro rumen fermentation was used in this study with four treatment groups: control (CON), fumarate (FA), nitroglycerin (NG) and fumarate plus nitroglycerin (FN). Real-time PCR and 16S rRNA gene sequencing were used to analyze microbiota. The results showed that nitroglycerin completely inhibited methane production and that this resulted in hydrogen accumulation. Fumarate decreased the hydrogen accumulation and improved the rumen fermentation parameters. Fumarate increased the concentration of propionate and microbial crude protein, and decreased the ratio of acetate to propionate in FN. Fumarate, nitroglycerin and their combination did not affect the abundance of bacteria, protozoa and anaerobic fungi, but altered archaea. The PCoA showed that the bacterial (Anosim, R = 0.747, p = 0.001) and archaeal communities (Anosim, R = 0.410, p = 0.005) were different among the four treatments. Compared with CON, fumarate restored Bacteroidetes, Firmicutes, Spirochaetae, Actinobacteria, Unclassified Ruminococcaceae, Streptococcus, Treponema and Bifidobacterium in relative abundance in FN, but did not affect Succinivibrio, Ruminobacter and archaeal taxa. The results indicated that fumarate alleviated the depressed rumen fermentation caused by the inhibition of methanogenesis by nitroglycerin. This may potentially provide an alternative way to use these chemicals to mitigate methane emission in ruminants.

Effects of Cashew Nut Shell Liquid on Hindgut Fermentation and Microbiota of Chickens

Cashew nut shell liquid (CNSL), a feed additive for chickens, was evaluated for its influence on the hindgut environment by determining fermentation and bacterial profiles using cecal contents, fecal slurry and pure cultures. A farm-scale study showed that CNSL feeding to broiler chickens from 0 to 42 days of age improved body weight gain and lowered mortality. Cecal levels of short chain fatty acids increased with CNSL feeding, while ammonia and indole levels decreased. Feeding CNSL decreased the relative abundance of cecal bacteria belonging to some clostridial groups and Ruminococcaceae. In particular, Clostridium perfringens was undetectable following CNSL feeding. A pure culture study showed that CNSL (≥ 6.25 μg/ml) inhibited C. perfringens growth, accompanied by cell surface disruption based on electron microscopic observation. Fermentation profiles of slurry cultures prepared from feces of chickens were altered by CNSL supplementation toward less ammonia production. The lowered ammonia was correlated positively with the abundance of unclassified Lachnospiraceae and unclassified Ruminococcaceae, and negatively with unclassified Enterobacteriaceae and Sutterella. These results suggest that CNSL could exert its beneficial influence on the hindgut health of chickens through impacting the microbiota.

Glucogenic and lipogenic diets affect in vitro ruminal microbiota and metabolites differently.

This study was conducted to evaluate the effects of two glucogenic diets (C: ground corn and corn silage; S: steam-flaked corn and corn silage) and a lipogenic diet (L: sugar beet pulp and alfalfa silage) on the ruminal bacterial and archaeal structures, the metabolomic products, and gas production after 48 h in vitro fermentation with rumen fluid of dairy cows. Compared to the C and S diets, the L dietary treatment leaded to a lower dry matter digestibility (DMD), lower propionate production and ammonia-nitrogen concentration. The two glucogenic diets performed worse in controlling methane and lactic acid production compared to the L diet. The S diet produced the greatest cumulative gas volume at any time points during incubation compared to the C and L diet. The metabolomics analysis revealed that the lipid digestion especially the fatty acid metabolism was improved, but the amino acid digestion was weakened in the L treatment than in other treatments. Differences in rumen fermentation characteristics were associated with (or resulting from) changes in the relative abundance of bacterial and archaeal genera. The rumen fluid fermented with L diet had a significantly higher number of cellulolytic bacteria, including the genera of Ruminococcus, Butyrivibrio, Eubacterium, Lachnospira, unclassified Lachnospiraceae, and unclassified Ruminococcaceae. The relative abundances of amylolytic bacteria genera including Selenomonas_1, Ruminobacter, and Succinivibrionaceae_UCG-002 were higher in samples for diets C and S. The results indicated that the two glucogenic diets leaded to a higher relative abundance of bacteria which functions in succinate pathway resulting in a higher propionate production. The steam-flaked corn diet had a higher gas production and lower level of metabolites in fatty acids and amino acids. Most highly abundant bacteria were observed to be not sensitive to dietary alterations of starch and fiber, except for several amylolytic bacteria and cellulolytic bacteria. These finding offered new insights on the digesting preference of ruminal bacteria, which can assist to improve the rumen functioning.

Cow's microbiome from antepartum to postpartum: A long-term study covering two physiological challenges.

Little is known about the interplay between the ruminant microbiome and the host during challenging events. This long-term study investigated the ruminal and duodenal microbiome and metabolites during calving as an individual challenge and a lipopolysaccharide-induced systemic inflammation as a standardized challenge. Strong inter- and intra-individual microbiome changes were noted during the entire trial period of 168 days and between the 12 sampling time points. Bifidobacterium increased significantly at 3 days after calving. Both challenges increased the intestinal abundance of fiber-associated taxa, e.g., Butyrivibrio and unclassified Ruminococcaceae. NMR analyses of rumen and duodenum samples identified up to 60 metabolites out of which fatty and amino acids, amines, and urea varied in concentrations triggered by the two challenges. Correlation analyses between these parameters indicated a close connection and dependency of the microbiome with its host. It turns out that the combination of phylogenetic with metabolite information supports the understanding of the true scenario in the forestomach system. The individual stages of the production cycle in dairy cows reveal specific criteria for the interaction pattern between microbial functions and host responses.

Longitudinal Reduction in Diversity of Maternal Gut Microbiota During Pregnancy Is Observed in Multiple Low-Resource Settings: Results From the Women First Trial.

ObjectiveTo characterize the changes in gut microbiota during pregnancy and determine the effects of nutritional intervention on gut microbiota in women from sub-Saharan Africa (the Democratic Republic of the Congo, DRC), South Asia (India and Pakistan), and Central America (Guatemala).MethodsPregnant women in the Women First (WF) Preconception Maternal Nutrition Trial were included in this analysis. Participants were randomized to receive a lipid-based micronutrient supplement either ≥3 months before pregnancy (Arm 1); started the same intervention late in the first trimester (Arm 2); or received no nutrition supplements besides those self-administered or prescribed through local health services (Arm 3). Stool and blood samples were collected during the first and third trimesters. Findings presented here include fecal 16S rRNA gene-based profiling and systemic and intestinal inflammatory biomarkers, including alpha (1)-acid glycoprotein (AGP), C-reactive protein (CRP), fecal myeloperoxidase (MPO), and calprotectin.ResultsStool samples were collected from 640 women (DRC, n = 157; India, n = 102; Guatemala, n = 276; and Pakistan, n = 105). Gut microbial community structure did not differ by intervention arm but changed significantly during pregnancy. Richness, a measure of alpha-diversity, decreased over pregnancy. Community composition (beta-diversity) also showed a significant change from first to third trimester in all four sites. Of the top 10 most abundant genera, unclassified Lachnospiraceae significantly decreased in Guatemala and unclassified Ruminococcaceae significantly decreased in Guatemala and DRC. The change in the overall community structure at the genus level was associated with a decrease in the abundances of certain genera with low heterogeneity among the four sites. Intervention arms were not significantly associated with inflammatory biomarkers at 12 or 34 weeks. AGP significantly decreased from 12 to 34 weeks of pregnancy, whereas CRP, MPO, and calprotectin did not significantly change over time. None of these biomarkers were significantly associated with the gut microbiota diversity.ConclusionThe longitudinal reduction of individual genera (both commensals and potential pathogens) and alpha-diversity among all sites were consistent and suggested that the effect of pregnancy on the maternal microbiota overrides other influencing factors, such as nutrition intervention, geographical location, diet, race, and other demographical variables.

Effects of calcium-magnesium carbonate and calcium-magnesium hydroxide as supplemental sources of magnesium on ruminal microbiome.

Our objective was to evaluate the inclusion of calcium-magnesium carbonate [CaMg(CO3)2] and calcium-magnesium hydroxide [CaMg(OH)4] in corn silage-based diets and their impact on ruminal microbiome. Our previous work showed a lower pH and molar proportion of butyrate from diets supplemented with [CaMg(CO3)2] compared to [CaMg(OH)4]; therefore, we hypothesized that ruminal microbiome would be affected by Mg source. Four continuous culture fermenters were arranged in a 4 × 4 Latin square with the following treatments defined by the supplemental source of Mg: 1) Control (100% MgO, plus sodium sesquicarbonate as a buffer); 2) CO3 [100% CaMg(CO3)2]; 3) OH [100% CaMg(OH)4]; and 4) CO3/OH [50% Mg from CaMg(CO3)2, 50% Mg from CaMg(OH)4]. Diet nutrient concentration was held constant across treatments (16% CP, 30% NDF, 1.66 MCal NEl/kg, 0.67% Ca, and 0.25% Mg). We conducted four fermentation periods of 10 d, with the last 3 d for collection of samples of solid and liquid digesta effluents for DNA extraction. Overall, 16 solid and 16 liquid samples were analyzed by amplification of the V4 variable region of bacterial 16S rRNA. Data were analyzed with R and SAS to determine treatment effects on taxa relative abundance of liquid and solid fractions. Correlation of butyrate molar proportion with taxa relative abundance was also analyzed. Treatments did not affect alpha and beta diversities or relative abundance of phylum, class and order in either liquid or solid fractions. At the family level, relative abundance of Lachnospiraceae in solid fraction was lower for CO3 and CO3/OH compared to OH and Control (P < 0.01). For genera, abundance of Butyrivibrio (P = 0.01) and Lachnospiraceae ND3007 (P < 0.01) (both from Lachnospiraceae family) was lower and unclassified Ruminococcaceae (P = 0.03) was greater in CO3 than Control and OH in solid fraction; while abundance of Pseudobutyrivibrio (P = 0.10) and Lachnospiraceae FD2005 (P = 0.09) (both from Lachnospiraceae family) and Ruminobacter (P = 0.09) tended to decrease in CO3 compared to Control in liquid fraction. Butyrate molar proportion was negatively correlated to Ruminococcaceae (r = –0.55) in solid fraction and positively correlated to Pseudobutyrivibrio (r = 0.61) and Lachnospiraceae FD2005 (r = 0.61) in liquid. Our results indicate that source of Mg has an impact on bacterial taxa associated with ruminal butyrate synthesis, which is important for epithelial health and fatty acid synthesis.