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Animal Microbiome Apr 2024Post weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide. New regulations in the EU limit the...
BACKGROUND
Post weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide. New regulations in the EU limit the use of in-feed antibiotics (Ab) and therapeutic zinc oxide (ZnO) to prevent PWD. New approaches to control PWD are needed, and understanding the role of the microbiota in this context is key. In this study, shotgun metagenome sequencing was used to describe the taxonomic and functional evolution of the faecal microbiota of the piglet during the first two weeks post weaning within three experimental groups, Ab, ZnO and no medication, on commercial farms using antimicrobials regularly in the post weaning period.
RESULTS
Diversity was affected by day post weaning (dpw), treatment used and diarrhoea but not by the farm. Microbiota composition evolved towards the dominance of groups of species such as Prevotella spp. at day 14dpw. ZnO inhibited E. coli overgrowth, promoted higher abundance of the family Bacteroidaceae and decreased Megasphaera spp. Animals treated with Ab exhibited inconsistent taxonomic changes across time points, with an overall increase of Limosilactobacillus reuteri and Megasphaera elsdenii. Samples from non-medicated pigs showed virulence-related functions at 7dpw, and specific ETEC-related virulence factors were detected in all samples presenting diarrhoea. Differential microbiota functions of pigs treated with ZnO were related to sulphur and DNA metabolism, as well as mechanisms of antimicrobial and heavy metal resistance, whereas Ab treated animals exhibited functions related to antimicrobial resistance and virulence.
CONCLUSION
Ab and particularly ZnO maintained a stable microbiota composition and functionality during the two weeks post weaning, by limiting E. coli overgrowth, and ultimately preventing microbiota dysbiosis. Future approaches to support piglet health should be able to reproduce this stable gut microbiota transition during the post weaning period, in order to maintain optimal gut physiological and productive conditions.
PubMed: 38627869
DOI: 10.1186/s42523-024-00306-7 -
AMB Express Apr 2024This research aimed to investigate effects of different yeast culture (YC) levels on in vitro fermentation characteristics and bacterial and fungal community under high...
This research aimed to investigate effects of different yeast culture (YC) levels on in vitro fermentation characteristics and bacterial and fungal community under high concentrate diet. A total of 5 groups were included in the experiment: control group without YC (CON), YC1 (0.5% YC proportion of substrate dry matter), YC2 (1%), YC3 (1.5%) and YC4 (2%). After 48 h of fermentation, the incubation fluids and residues were collected to analyze the ruminal fermentation parameters and bacterial and fungal community. Results showed that the ruminal fluid pH of YC2 and YC4 groups was higher (P < 0.05) than that of CON group. Compared with CON group, the microbial protein, propionate and butyrate concentrations and cumulative gas production at 48 h of YC2 group were significantly increased (P < 0.05), whereas an opposite trend of ammonia nitrogen and lactate was observed between two groups. Microbial analysis showed that the Chao1 and Shannon indexes of YC2 group were higher (P < 0.05) than those of CON group. Additionally, YC supplementation significantly decreased (P < 0.05) Succinivibrionaceae_UCG-001, Streptococcus bovis and Neosetophoma relative abundances. An opposite tendency of Aspergillus abundance was found between CON and YC treatments. Compared with CON group, the relative abundances of Prevotella, Succiniclasticum, Butyrivibrio and Megasphaera elsdenii were significantly increased (P < 0.05) in YC2 group, while Apiotrichum and unclassified Clostridiales relative abundances were decreased (P < 0.05). In conclusion, high concentrate substrate supplemented with appropriate YC (1%) can improve ruminal fermentation and regulate bacterial and fungal composition.
PubMed: 38622373
DOI: 10.1186/s13568-024-01692-6 -
Ecotoxicology and Environmental Safety May 2024Calotropis gigantea (Giant milkweed, GM) has the potential to be utilized as a new feed additive for ruminants, however, the presence of unpalatable or toxic compounds...
Calotropis gigantea (Giant milkweed, GM) has the potential to be utilized as a new feed additive for ruminants, however, the presence of unpalatable or toxic compounds decreases animal feed intake. This study aimed to valorize GM as a potential new feed resource through the chemical and microbial biotransformation of toxic compounds that will henceforth, make the plant palatable for cows. After GM's ensiling using fermentative bacteria, the plant was sampled for UHPLC-MS/MS to analyse the metabolomic changes. Illumina Miseq of the 16 S rRNA fragment genes and ITS1 were used to describe the microbial composition and structure colonizing GM silage and contributing to the biodegradation of toxic compounds. Microbial functions were predicted from metataxonomic data and KEGG pathways analysis. Eight Holstein dairy cows assigned in a cross-over design were supplemented with GM and GM silage to evaluate palatability and effects on milk yield and milk protein. Cows were fed their typical diet prior to the experiment (positive control). After ensiling, 23 flavonoids, 47 amino acids and derivatives increased, while the other 14 flavonoids, 9 amino acids and derivatives decreased, indicating active metabolism during the GM ensiling process. Lactobacillus buchneri, Bacteroides ovatus, and Megasphaera elsdenii were specific to ensiled GM and correlated to functional plant metabolites, while Sphingomonas paucimobilis and Staphylococcus saprophyticus were specific to non-ensiled GM and correlated to the toxic metabolite 5-hydroxymethylfurfural."Xenobiotics biodegradation and metabolism", "cancer overview" and "neurodegenerative disease" were the highly expressed microbial KEGG pathways in non-ensiled GM. Non-ensiled GM is unpalatable for cows and drastically reduces the animal's feed intake, whereas ensiled GM does not reduce feed intake, milk yield and milk protein. This study provides essential information for sustainable animal production by valorizing GM as a new feed additive.
Topics: Animals; Cattle; Female; Silage; Animal Feed; Milk; Lactation; Diet
PubMed: 38581911
DOI: 10.1016/j.ecoenv.2024.116292 -
Frontiers in Cellular and Infection... 2024Post-weaning diarrhoea (PWD) is a multifactorial disease that affects piglets after weaning, contributing to productive and economic losses. Its control includes the use... (Review)
Review
INTRODUCTION
Post-weaning diarrhoea (PWD) is a multifactorial disease that affects piglets after weaning, contributing to productive and economic losses. Its control includes the use of in-feed prophylactic antibiotics and therapeutic zinc oxide (ZnO), treatments that, since 2022, are no longer permitted in the European Union due to spread of antimicrobial resistance genes and pollution of soil with heavy metals. A dysbiosis in the microbiota has been suggested as a potential risk factor of PWD onset. Understanding pig's microbiota development around weaning and its changes in response to ZnO and antibiotics is crucial to develop feasible alternatives to prophylactic and metaphylactic antimicrobial use.
METHODS
This study used shotgun metagenomic sequencing to investigate the environmental and faecal microbiota on 10 farms using (Treated) or not using (ZnO-free) in-feed antibiotics and ZnO during the first 14 days post-weaning (dpw). Environmental samples from clean pens were collected at weaning day (0dpw), and faecal samples at 0, 7 and 14dpw. Diarrhoeic faecal samples were collected at 7dpw when available.
RESULTS
The analysis of data revealed that the faecal microbiota composition and its functionality was impacted by the sampling time point (microbiota maturation after weaning) but not by the farm environment. Treatment with antibiotics and ZnO showed no effects on diversity indices while the analyses of microbiota taxonomic and functional profiles revealed increased abundance of taxa and metabolic functions associated with or different species of . on the Treated farms, and with and on the ZnO-free farms. The analysis of diarrhoea samples revealed that the treatment favoured the microbiota transition or maturation from 0dpw to 14dpw in Treated farms, resembling the composition of healthy animals, when compared to diarrhoea from ZnO-free farms, which were linked in composition to 0dpw samples.
DISCUSSION
The results provide a comprehensive overview of the beneficial effects of ZnO and antibiotics in PWD in the microbiota transition after weaning, preventing the overgrowth of pathogens such as pathogenic and revealing the key aspects in microbiota maturation that antibiotics or ZnO alternatives should fulfil.
Topics: Swine; Animals; Escherichia coli; Anti-Bacterial Agents; Zinc Oxide; Diarrhea; Microbiota
PubMed: 38384302
DOI: 10.3389/fcimb.2024.1354449 -
Microorganisms Jan 2024The Gram-negative, strictly anaerobic bacterium was first isolated from the rumen in 1953 and is common in the mammalian gastrointestinal tract. Its ability to use... (Review)
Review
The Gram-negative, strictly anaerobic bacterium was first isolated from the rumen in 1953 and is common in the mammalian gastrointestinal tract. Its ability to use either lactate or glucose as its major energy sources for growth has been well documented, although it can also ferment amino acids into ammonia and branched-chain fatty acids, which are growth factors for other bacteria. The ruminal abundance of usually increases in animals fed grain-based diets due to its ability to use lactate (the product of rapid ruminal sugar fermentation), especially at a low ruminal pH (<5.5). has been proposed as a potential dietary probiotic to prevent ruminal acidosis in feedlot cattle and high-producing dairy cows. However, this bacterium has also been associated with milk fat depression (MFD) in dairy cows, although proving a causative role has remained elusive. This review summarizes the unique physiology of this intriguing bacterium and its functional role in the ruminal community as well as its role in the health and productivity of the host animal. In addition to its effects in the rumen, the ability of to produce C-C carboxylic acids-potential precursors for industrial fuel and chemical production-is examined.
PubMed: 38276203
DOI: 10.3390/microorganisms12010219 -
Food Chemistry: X Mar 2024Tea ( L.) flower polysaccharides (TFPS) have various health-promoting functions. In the present work, the structure of a purified TFPS fraction, namely TFPS-1-3p, and...
Tea ( L.) flower polysaccharides (TFPS) have various health-promoting functions. In the present work, the structure of a purified TFPS fraction, namely TFPS-1-3p, and its digestive properties were investigated. The results demonstrated that TFPS-1-3p was a typical heteropolysaccharide consisting of rhamnose (Rha), arabinose (Ara), galactose (Gal) and galacturonic acid (GalA) with a molecular weight of 47.77 kDa. The backbone of TFPS-1-3p contained → 4)-α-d-GalA(-6-OMe)-(1 → 4)-α-GalA-(1 → and → 4)-α-d-GalA(-6-OMe)-(1 → 2,4)-α-l-Rha-(1 → linkages. The branch linkages in TFPS-1-3p contained → 6)-β-d-Gal-(1→, →3,6)-β-d-Gal-(1→, →5)-α-l-Ara-(1 → and → 3,5)-α-l-Ara-(1 →. Subsequently, TFPS-1-3p could not be degraded under simulated human gastrointestinal conditions but could be of use to human fecal microbes, thereby lowering the pH and increasing the production of short-chain fatty acids (SCFAs) of the gut microenvironment and altering the composition of the gut microbiota. The relative abundance of , and increased significantly, potentially contributing to the degradation of TFPS-1-3p.
PubMed: 38178927
DOI: 10.1016/j.fochx.2023.101058 -
Bioresource Technology Feb 2024The objective was to investigate the impact of the bioaugmentation on chain elongation process using glycerol, lactate and lactose as substrates in an open culture...
The objective was to investigate the impact of the bioaugmentation on chain elongation process using glycerol, lactate and lactose as substrates in an open culture fermentation. In the batch trials the highest selectivity for chain elongation product, i.e. caproate, was observed in trials inoculated with co-culture of Megasphaera elsdenii and Eubacterium limosum grown on glycerol (28.6%), and in non-bioaugmented open culture run on lactose + lactate (14.8%). The results showed that E. limosum, out of two bioaugmented strains, was able to survive in the open culture. A continuous open culture fermentation of glycerol led to caproate and 1,3-propanediol (1,3-PDO) formation, while lactate addition led to 1,3-PDO and short chain carboxylates production. Moving the process into batch mode triggered even-carbon chain elongation. Presence of E. limosum promoted odd-carbon chain elongation and valerate production. Imaging flow cytometry combined with machine learning enabled the discrimination of Eubacterium cells from other microbial strains during the process.
Topics: Lactic Acid; Caproates; Carboxylic Acids; Glycerol; Lactose; Fermentation; Propylene Glycol; Carbon; Propylene Glycols
PubMed: 38042435
DOI: 10.1016/j.biortech.2023.130123 -
Translational Animal Science 2023Our objective was to evaluate the effects of combinations of and as direct-fed microbials (DFM) on ruminal microbiome during an acute acidosis challenge in a...
Our objective was to evaluate the effects of combinations of and as direct-fed microbials (DFM) on ruminal microbiome during an acute acidosis challenge in a continuous culture system. Treatments provided a DFM dose of 1 × 10 colony-forming unit (CFU)/mL, as follows: control (no DFM), YM1 ( and strain 1), YM2 ( and strain 2), and YMM ( and half of the doses of strains 1 and 2). We conducted four experimental periods of 11 d, which consisted of non-acidotic days (1 to 8) and acidotic challenge days (9 to 11) to establish acute ruminal acidosis conditions with a common basal diet containing 12% neutral detergent fiber and 58% starch. Treatments were applied from days 8 to 11, and samples of liquid and solid-associated bacteria were collected on days 9 to 11. Overall, 128 samples were analyzed by amplification of the V4 region of bacterial 16S rRNA, and data were analyzed with R and SAS for alpha and beta diversity, taxa relative abundance, and correlation of taxa abundance with propionate molar proportion. We observed a lower bacterial diversity (Shannon index, = 0.02) when YM1 was added to the diet in comparison to the three other treatments. Moreover, compared to control, addition of YM1 to the diet increased relative abundance of phylum ( = 0.05) and family ( = 0.05) in the solid fraction and tended to increase abundance of family ( = 0.10) and genus ( = 0.09) in the liquid fraction. Correlation analysis indicated a positive association between propionate molar proportion and relative abundance of ( = 0.36, = 0.04) and ( = 0.36, = 0.05) in the solid fraction. The inclusion of YM1 in high-grain diets with a high starch content resulted in greater abundance of bacteria involved in succinate synthesis which may have provided the substrate for the greater propionate synthesis observed.
PubMed: 38023425
DOI: 10.1093/tas/txad123 -
Microbiome Sep 2023Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a cerebral small vessel disease that carries mutations in NOTCH3....
BACKGROUND
Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a cerebral small vessel disease that carries mutations in NOTCH3. The clinical manifestations are influenced by genetic and environmental factors that may include gut microbiome.
RESULTS
We investigated the fecal metagenome, fecal metabolome, serum metabolome, neurotransmitters, and cytokines in a cohort of 24 CADASIL patients with 28 healthy household controls. The integrated-omics study showed CADASIL patients harbored an altered microbiota composition and functions. The abundance of bacterial coenzyme A, thiamin, and flavin-synthesizing pathways was depleted in patients. Neurotransmitter balance, represented by the glutamate/GABA (4-aminobutanoate) ratio, was disrupted in patients, which was consistent with the increased abundance of two major GABA-consuming bacteria, Megasphaera elsdenii and Eubacterium siraeum. Essential inflammatory cytokines were significantly elevated in patients, accompanied by an increased abundance of bacterial virulence gene homologs. The abundance of patient-enriched Fusobacterium varium positively correlated with the levels of IL-1β and IL-6. Random forest classification based on gut microbial species, serum cytokines, and neurotransmitters showed high predictivity for CADASIL with AUC = 0.89. Targeted culturomics and mechanisms study further showed that patient-derived F. varium infection caused systemic inflammation and behavior disorder in Notch3 mice potentially via induction of caspase-8-dependent noncanonical inflammasome activation in macrophages.
CONCLUSION
These findings suggested the potential linkage among the brain-gut-microbe axis in CADASIL. Video Abstract.
Topics: Animals; Mice; CADASIL; Gastrointestinal Microbiome; Mental Disorders; Cytokines; gamma-Aminobutyric Acid
PubMed: 37684694
DOI: 10.1186/s40168-023-01638-3 -
Journal of Food Protection Sep 2023Feedlot cattle commonly shed the foodborne pathogen Escherichia coli O157:H7 in their feces. Megasphaera elsdenii (ME), a lactic acid-utilizing bacterium, is commonly...
Feedlot cattle commonly shed the foodborne pathogen Escherichia coli O157:H7 in their feces. Megasphaera elsdenii (ME), a lactic acid-utilizing bacterium, is commonly administered to cattle to avoid lactate accumulation in the rumen and to control ruminal acidosis. The impact of administering ME on foodborne pathogen prevalence, specifically E. coli O157:H7, has not been explored. The purpose of this study was to quantify E. coli O157:H7 prevalence in finishing cattle administered ME. Cattle (n = 448) were assigned to treatments in a randomized complete block design with repeated measurements over two sampling periods. Treatments were arranged as a 2 × 2 factorial containing: ruminally protected lysine (RPL; included for a complementary study) fed at 0% or 0.45% of diet dry matter; with or without ME. Freeze-dried ME was administered as an oral drench (1 × 10 CFU/steer on day one) and then top dressed onto basal diets (1 × 10 CFU/steer) daily thereafter. Rectoanal mucosal swabs (RAMS) were obtained from animals before harvest to determine the E. coli O157:H7 prevalence. The inclusion of RPL (P = 0.2136) and ME (P = 0.5012) did not impact E. coli O157:H7 prevalence, and RPL was not included in any significant interactions (P > 0.05). A significant interaction was observed between ME and sampling period (P = 0.0323), indicating that the effect of ME on E. coli O157:H7 prevalence varied over the sampling period. A diet containing ME reduced the odds of E. coli O157:H7 prevalence by 50% during sampling period 1 (8.0% and 14.7% for cattle with and without ME, respectively) and increased the odds by 23% during sampling period 2 (10.8% and 8.9% for cattle with and without ME, respectively). Administering ME in cattle diets did not impact E. coli O157:H7 in feedlot cattle. This is the first study to investigate the use of ME as a preharvest food safety intervention in cattle, and additional research is necessary to determine the efficacy.
Topics: Animals; Cattle; Male; Animal Feed; Cattle Diseases; Colony Count, Microbial; Escherichia coli Infections; Escherichia coli O157; Feces; Megasphaera elsdenii; Prevalence; Probiotics; Sheep
PubMed: 37479183
DOI: 10.1016/j.jfp.2023.100133