Presence of sourdough lactic acid bacteria in commercial total mixed ration silage as revealed by denaturing gradient gel electrophoresis analysis

Fermented Total Mixed Ration Alters Rumen Fermentation Parameters and Microbiota in Dairy Cows

This study aimed to determine changes and interactions of ruminal microbiota and chemical parameters in dairy cows fed FTMR. Twelve multiparous Holstein dairy cows (Body weight = 616 ± 13.4 kg; day in milk = 106 ± 7.55 d; and parity = 2.31 ± 0.49; mean ± standard deviation) were divided randomly into two treatments depending on the day in milk, milk production, and parity. The two treatments were: (1) total mixed ration (TMR) and (2) FTMR. Illumina MiSeq sequencing was used to explore the changes in the ruminal microbiota. The results revealed that the bacterial and fungal diversity of the FTMR group were significantly higher than the TMR group. The predominant microbiota phyla in the bacteria and fungi showed significant differences between TMR and FTMR, as follows: Verrucomicrobia (p = 0.03) and Tenericutes (p = 0.01), Ascomycota (p = 0.04) and Basidiomycota (p = 0.04). The dominant bacterial genera in the bacteria, fungi, protozoan, and archaea that showed significant differences between TMR and FTMR were Unclassified_Bacteroidales (p = 0.02), Unclassified_RFP12 (p = 0.03), Candida (p = 0.0005), Bullera (p = 0.002), Cryptococcus (p = 0.007), and Ostracodinium (p = 0.01). LefSe analysis was performed to reveal the biomarker genera of the rumen microbiota community (bacteria, fungi, protozoan, and archaea) in the TMR and FTMR were the genera Shuttleworthia, Ruminococcus, Cryptococcus, Mycosphaerella, Bullera, Candida, and Ostracodinium. NH3-N concentration (p < 0.0001), total VFA concentration (p = 0.003), and molar proportion in total VFA of acetate (p = 0.01) were higher for the cows fed FTMR compared with the cows fed the TMR. Several bacterial genera showed significant correlations with rumen fermentation parameters. The genus Unclassified_Bacteroidales and Bullera were positively correlated with total volatile fatty acids (VFA) and acetate, whereas Candida and Ostracodinium showed negative correlations. Meanwhile, propionate was positively correlated with Candida and negatively correlated with Bullera. The PICRUSt functional profile prediction indicated that the xenobiotics biodegradation and metabolism, the lipid, amino acid, terpenoids, and polyketides metabolisms of the FTMR group were significantly higher than that of the TMR group. The results imply that FTMR can increase lipid and amino acid metabolism, and modulate the rumen microbiome and improve ruminal fermentation.

Comparative Genomics of Lentilactobacillus parabuchneri isolated from dairy, KEM complex, Makgeolli, and Saliva Microbiomes

BACKGROUND

Lentilactobacillus parabuchneri is of particular concern in fermented food bioprocessing due to causing unwanted gas formation, cracks, and off-flavor in fermented dairy foods. This species is also a known culprit of histamine poisonings because of decarboxylating histidine to histamine in ripening cheese. Twenty-eight genomes in NCBI GenBank were evaluated via comparative analysis to determine genomic diversity within this species and identify potential avenues for reducing health associated risks and economic losses in the food industry caused by these organisms.

RESULT

Core genome-based phylogenetic analysis revealed four distinct major clades. Eight dairy isolates, two strains from an unknown source, and a saliva isolate formed the first clade. Three out of five strains clustered on clade 2 belonged to dairy, and the remaining two strains were isolated from the makgeolli and Korean effective microorganisms (KEM) complex. The third and fourth clade members were isolated from Tete de Moine and dairy-associated niches, respectively. Whole genome analysis on twenty-eight genomes showed ~ 40% of all CDS were conserved across entire strains proposing a considerable diversity among L. parabuchneri strains analyzed. After assigning CDS to their corresponding function, ~ 79% of all strains were predicted to carry putative intact prophages, and ~ 43% of the strains harbored at least one plasmid; however, all the strains were predicted to encode genomic island, insertion sequence, and CRISPR-Cas system. A type I-E CRISPR-Cas subgroup was identified in all the strains, with the exception of DSM15352, which carried a type II-A CRISPR-Cas system. Twenty strains were predicted to encode histidine decarboxylase gene cluster that belongs to not only dairy but also saliva, KEM complex, and unknown source. No bacteriocin-encoding gene(s) or antibiotic resistome was found in any of the L. parabuchneri strains screened.

CONCLUSION

The findings of the present work provide in-depth knowledge of the genomics of L. parabuchneri by comparing twenty-eight genomes available to date. For example, the hdc gene cluster was generally reported in cheese isolates; however, our findings in the current work indicated that it could also be encoded in those strains isolated from saliva, KEM complex, and unknown source. We think prophages are critical mobile elements of L. parabuchneri genomes that could pave the way for developing novel tools to reduce the occurrence of this unwanted species in the food industry.

Bacterial and fungal microbiota of total mixed ration silage stored at various temperatures

AIMS

To obtain insights into how bacterial and fungal microbiota and fermentation products composition are affected by storage temperature for TMR silage, which can be manufactured year-round.

METHODS AND RESULTS

TMR silage was stored at 10°C, 25°C, ambient temperature (AT; 20-35°C), and 40°C. Lactic acid production was delayed when stored at 10°C, and acid production stagnated after 2 weeks when stored at 40°C. The patterns of acetic acid and ethanol production were inversely related, with ethanol production promoted at 10°C and 25°C and acetic acid production promoted at AT and 40°C. The bacterial diversity was reduced in TMR silage with high lactic acid and acetic acid content, and the fungal diversity was reduced in TMR silage with high ethanol content.

CONCLUSIONS

The intensity of lactic acid production was accounted for by the high abundance of Lactobacillus, and its stagnated production at a substantially high storage temperature was related to an increased abundance of Bacillus. The enhanced production of acetic acid or ethanol can be explained by differences in the fungal microbiota.

SIGNIFICANCE AND IMPACT OF THE STUDY

The integrated analysis of bacterial and fungal microbiota can provide in-depth insights into the impact of storage temperature on TMR silage fermentation.

Storage Temperature Is More Effective Than Lactic Acid Bacteria Inoculations in Manipulating Fermentation and Bacterial Community Diversity, Co-Occurrence and Functionality of the Whole-Plant Corn Silage

The objective of this study was to investigate effects of different lactic acid bacteria (LAB) on the fermentation process of whole-plant corn silage stored at different temperatures based on bacterial community successions, interaction networks, and predicted functions. Before ensiling, whole-plant corn was inoculated with L. plantarum (LP) or L. buchneri (LB) and the silage bags were stored at 20 or 30°C, and sampled after 0.5, 1, 3, 7, 14, and 60 d of ensiling. The higher abundances of Leuconostoc, Pedicoccus and Weissella were observed in silage stored at 30°C after 12 h of ensiling, thereby rapidly decreased pH to about 4.5. According to meta-network analysis, the bacterial communities were more sensitive to storage temperature than LAB inoculants during whole-plant corn ensiling. Species of Lactobacillus and Weissella were sensitive to 30°C, while Leuconostoc species were sensitive to 20°C in whole-plant corn silage. The storage temperature of 30°C decreased bacterial diversity and network complexity of whole-plant corn silage compared with 20°C. Additionally, LP inoculation changed the bacterial community successions during the early and middle ensiling periods, while LB inoculation affected bacterial community successions in the later stage of ensiling. The metabolic pathways of bacterial community were totally different in LB-inoculated silage from that in control and LP-inoculated silage. As the bacterial compositions became simple along with the ensiling process, the functional structure of bacterial community became simplified as well. In general, the storage temperature had a greater impact on the fermentation characteristics, bacterial community and predicted function of whole-plant corn silage compared with LAB inoculations.

IMPORTANCE Increased understanding of effects of regulation measures on whole-plant corn silage is important from bacterial community succession, interaction network and predicted functions. According to alpha diversity and meta co-occurrence network, the bacterial communities were more sensitive to storage temperature than LAB inoculants during whole-plant corn ensiling. The storage temperature of 30°C decreased bacterial diversity and network complexity of whole-plant corn silage compared with 20°C. In addition, 30°C promoted the initiation of LP and LB inoculants, and 20°C was conducive to the long-term growth of LP and LB inoculants. According to the changes of bacterial community and predicated functions, it was further confirmed that the effect of LB inoculation was more obvious on whole-plant corn silage.

Effects of Replacing Ensiled-Alfalfa with Fresh-Alfalfa on Dynamic Fermentation Characteristics, Chemical Compositions, and Protein Fractions in Fermented Total Mixed Ration with Different Additives

Simple Summary

Alfalfa (Medicago sativa) is commonly used as a high-quality protein source in fermented total mixed ration (FTMR) for ruminants. This study evaluated the fermentation characteristics, chemical compositions, and protein fractions of FTMR using fresh-alfalfa as the main ingredients replacing ensiled-alfalfa. The results showed that fresh-alfalfa FTMR exhibited a similar pH, propionic acid content and neutral detergent fiber, nonprotein, and variable to slow protein and indigestible protein levels in comparison to ensiled-alfalfa FTMR. Therefore, the use of fresh-alfalfa as a main ingredient in FTMR is promising.

Abstract

Alfalfa (Medicago sativa) is one of the high protein ingredients of fermented total mixed ration (FTMR). Additionally, FTMR is widely used to satisfy the nutrition requirements of animals. This study was conducted to confirm the fermentation characteristics, chemical compositions and protein fractions changes when replacing ensiled-alfalfa with fresh-alfalfa in FTMR with additives. Three additives were separately applied to fresh-alfalfa total mixed ration (TMR) and ensiled-alfalfa TMR, including molasses (MOL), Lactobacillus plantarum (LP) and MOL plus LP (MOL+LP). The same volume of distilled water was sprayed onto the prepared TMR as performed for the control (CK). Each treatment included 18 repetitions and opened 3 repetitions at each fermenting day (1, 3, 7, 15, 30 and 60 d). The results showed that fresh-alfalfa FTMR (F-FTMR) exhibited slight changes in the fermentation characteristics during the first 7 d and showed similar trends in terms of the pH and organic acids content to ensiled-alfalfa FTMR (E-FTMR). The lactic acid contents of F-FTMR were significantly lower than those of E-FTMR at 60 d fermentation and the ammonia nitrogen contents were lower than E-FTMR during the entire fermenting period. The crude protein of the F-FTMR was enhanced after 60 d of fermenting. F-FTMR supplemented with MOL+LP exhibited a lower nonprotein nitrogen content, variable to slow protein and indigestible protein contents, and higher fast degradable protein and true protein degraded intermediately contents at 60 d fermenting, indicating that it effectively inhibited protein degradation.

Molecular typing tools for identifying and characterizing lactic acid bacteria: a review

Identification and classification of beneficial microbes is of the highest significance in food science and related industries. Conventional phenotypic approaches pose many challenges, and they may misidentify a target, limiting their use. Genotyping tools show comparatively better prospects, and they are widely used for distinguishing microorganisms. The techniques already employed in genotyping of lactic acid bacteria (LAB) are slightly different from one another, and each tool has its own advantages and disadvantages. This review paper compiles the comprehensive details of several fingerprinting tools that have been used for identifying and characterizing LAB at the species, sub-species, and strain levels. Notably, most of these approaches are based on restriction digestion, amplification using polymerase chain reaction, and sequencing. Nowadays, DNA sequencing technologies have made considerable progress in terms of cost, throughput, and methodology. A research journey to develop improved versions of generally applicable and economically viable tools for fingerprinting analysis is ongoing globally.

Microbial community and fermentation characteristic of Italian ryegrass silage prepared with corn stover and lactic acid bacteria

The bacterial community determined via PacBio single molecule, real-time sequencing technology (SMRT) and the fermentation characteristics of Italian ryegrass (IR, 82% moisture) silage prepared with corn stover (CS) were investigated. A selected strain of Lactobacillus plantarum (L694) and a commercial inoculant stain of Lactobacillus plantarum (LP) were used as additives. Lactic acid bacteria (LAB) effectively improved silage quality. After fermentation, Lactobacillus plantarum was the dominant species in IR + LP and IR + L694 treatments, which led to higher (P < 0.05) lactic acid and lower (P < 0.05) butyric acid production. Lactobacillus plantarum, Lactobacillus hammesii, Lactobacillus brevis, and Lactobacillus coryniformis were abundantly present in IR + CS + LP and IR + CS + L694 treatments, and acetic acid contents of these were higher (P < 0.05) than those of other silages. This study demonstrated that addition of CS and LAB can change the microbial community and influence the silage fermentation of IR, and PacBio SMRT reveals more specific microbial information.

Changes in nutrient composition and in vitro ruminal fermentation of total mixed ration silage stored at different temperatures and periods

BACKGROUND

Total mixed ration (TMR) is widely used for dairy cattle and needs to be prepared daily because it deteriorates rapidly. Ensiling TMR allows preservation and saves labour at the farm; however, silage fermentation may influence various nutritional components. The objectives of this study were to evaluate nutritional changes and in vitro rumen fermentation of TMR silage that was stored at different temperatures and durations on a laboratory scale in comparison with those of typical TMR before ensiling.

RESULTS

No distinct changes in crude protein (CP), neutral detergent fibre and non-fibrous carbohydrate contents were observed during silage fermentation. However, clear changes were observed in the soluble CP and soluble sugar fractions; solubilisation of the CP fraction in TMR silage was enhanced by prolonged storage and higher storage temperatures, and most soluble sugars were lost during ensiling. Short-chain fatty acid concentrations in the in vitro rumen from TMRs before and after ensiling were not significantly different; however, throughout incubation, NH3 -N concentrations from TMR silages were significantly higher than those from TMR before ensiling.

CONCLUSION

A higher ruminal NH3 -N concentration from TMR silage may be a result of a shortage of fermentable sugars and enhanced deamination of CP. Feeding TMR ensiled under a high temperature must be investigated to balance proteins and carbohydrates for rumen fermentation.

Identification of bacteria in total mixed ration silage produced with and without crop silage as an ingredient

As a forage source for total mixed ration (TMR) silage production, locally produced crop silage is now used in addition to imported hay. This type of TMR ensiling is regarded as a two-step fermentation process; hence, a survey was carried out to determine whether the bacteria in crop silage affect the subsequent TMR ensiling. Fermentation product contents and bacterial community were determined for TMR silage and its ingredient silages collected in August, October and November. August product contained corn, sorghum and Italian ryegrass silages, October product had wheat silage exclusively and November product did not include any crop silages. Acetic acid, lactic acid, 2,3-butanediol and ethanol were predominant fermentation products in corn, sorghum, Italian ryegrass and wheat silages, respectively. Robust lactic acid fermentation was seen in TMR silage, even if acetate-type and alcohol-type silages were mixed as ingredients. The finding that bacterial community of the TMR silage appeared unrelated to those of ingredient silage supported this. Silages of various fermentation types can therefore be formulated without interfering with lactate-type fermentation in TMR silage.

Effect of korean herbal medicine combined with a probiotic mixture on diarrhea-dominant irritable bowel syndrome: a double-blind, randomized, placebo-controlled trial

Introduction. Although combination therapy with herbal medicine and probiotics is gaining popularity for controlling diarrhea-dominant irritable bowel syndrome (D-IBS) symptoms, few studies have investigated its clinical effects. Materials and Methods. Fifty-three patients with D-IBS were randomly allocated into 1 of the following 4 groups: herbal medicine (Gwakhyangjeonggisan; GJS) plus probiotics (Duolac7S; DUO), GJS plus placebo DUO, placebo GJS plus DUO, and placebo GJS plus placebo DUO. The study period consisted of a 2-week run-in, 8 weeks of administration, and 2 weeks of follow-up. The primary outcomes were weekly adequate relief (AR) of overall IBS symptoms and the proportion of responders (PR) during the administration period. The secondary outcomes included individual IBS symptoms, stool assessment, and quality of life. Changes of intestinal microbiota and intestinal permeability were also analyzed. Results and Discussion. Weekly AR was not different among the 4 groups throughout the treatment period. However, the 3 treatment groups exhibited significant improvements in PR compared to the findings in the placebo group. In the intestinal microbiota assessment, herbal medicine and probiotics synergistically increased beneficial bacteria counts. Conclusion. Combination therapy with herbal medicine and probiotics appears to relieve overall IBS symptoms by synergistically increasing beneficial intestinal microbe counts.

Effects of storage temperature and ensiling period on fermentation products, aerobic stability and microbial communities of total mixed ration silage

AIMS

To examine how storage temperatures influence ensiling fermentation, aerobic stability and microbial communities of total mixed ration (TMR) silage.

METHODS AND RESULTS

Laboratory-scale silos were stored at 5, 15, 25 and 35°C for 10, 30 and 90 days. If silage was stored at 5°C, fermentation was weak until day 30, but acceptable lactic acid production was observed on day 90. The ethanol content was higher than the acetic acid content when stored at 15 and 25°C, whereas the ethanol content was lower when stored at 35 than at 25°C. Aerobic deterioration did not occur when silage was exposed to air at the same temperature at which it was stored. Although 10-day silages stored at 5 and 15°C deteriorated when the aerobic stability test was conducted at 25°C, heating was not observed in silages stored at 25 or 35°C or in any 90-day silages regardless of storage temperature. Denaturing gradient gel electrophoresis demonstrated that bands indicative of Lactobacillus plantarum and Lactobacillus delbrueckii were less prominent, while bands indicative of Lactobacillus panis became more distinct in silages stored at high temperatures. Bands of Kluyveromyces marxianus were seen exclusively in silages that were spoiled at 25°C.

CONCLUSION

High ambient temperature enhances acetic acid production in TMR silage. Lactobacillus panis may be associated with changes in the fermentation products due to differences in storage temperature.

SIGNIFICANCE AND IMPACT OF THE STUDY

The role of Lacto. panis in ensiling fermentation and aerobic stability is worth examining.

Effect of herbal extract granules combined with probiotic mixture on irritable bowel syndrome with diarrhea: study protocol for a randomized controlled trial

Background

Irritable bowel syndrome (IBS) is a chronic gastrointestinal disorder characterized by abdominal pain and change of bowel habits without organic disease. Many patients seek alternative IBS treatments because of the limitations of conventional treatments. Gwakhyangjeonggisan (GJS), a herbal formula, has long been used for alleviating diarrhea-predominant IBS (D-IBS) in traditional medicine. Duolac7S, which comprises 7 bacterial species as probiotics, has been frequently used for D-IBS. Although GJS and Duolac7S have been administered simultaneously in many D-IBS patients, no study has investigated the effects of GJS and Duolac7S combination therapy on D-IBS.

Methods/Design

The current trial is a randomized, double-blinded, placebo-controlled, 4-arm study. After a 2-week run-in period, 60 patients with D-IBS will be randomly assigned to one of the 4 combination groups consisting of GJS (water extract granules, 3 g/pack, 3 times a day) with Duolac7S (powder form, 1 capsule, 2 times a day) or their placebos and followed up for 2 weeks. The assigned treatments will last for 8 weeks. The primary outcomes are adequate relief of IBS pain and discomfort and the proportion of responders (on a weekly basis). The secondary outcomes are visual analog scale for IBS symptoms (on a daily basis), quality of life (at 0, 8, and 10 weeks), intestinal permeability, and composition of intestinal microbiota (at 0 and 8 weeks).

Discussion

The present study is designed to examine the safety and efficacy of GJS and Duolac7S combination therapy on D-IBS. Our study provides the clinical evidence of a new therapeutic strategy for D-IBS.

Trial registration

ClinicalTrials.gov NCT01342718 .