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Journal of Animal Science and... Jan 2024Stocker cattle diet and management influence beef cattle performance during the finishing stage, but knowledge of the dynamics of the rumen microbiome associated with...
BACKGROUND
Stocker cattle diet and management influence beef cattle performance during the finishing stage, but knowledge of the dynamics of the rumen microbiome associated with the host are lacking. A longitudinal study was conducted to determine how the feeding strategy from the stocker to the finishing stages of production affects the temporal dynamics of rumen microbiota. During the stocker phase, either dry hay or wheat pasture were provided, and three levels of monensin were administrated. All calves were then transported to a feedlot and received similar finishing diets with or without monensin. Rumen microbial samples were collected on d 0, 28, 85 during the stocker stage (S0, S28 and S85) and d 0, 14, 28, 56, 30 d before slaughter and the end of the trial during the finishing stage (F0, F14, F28, F56, Pre-Ba, and Final). The V4 region of the bacterial 16S rRNA gene of 263 rumen samples was sequenced.
RESULTS
Higher alpha diversity, including the number of observed bacterial features and the Shannon index, was observed in the stocker phase compared to the finishing phase. The bacterial amplicon sequence variants (ASVs) differentiating different sampling time points were identified. Dietary treatments during the stocker stage temporally impact the dynamics of rumen microbiota. For example, shared bacteria, including Bacteroidales (ASV19) and Streptococcus infantarius (ASV94), were significantly higher in hay rumen on S28, S85, and F0, while Bacteroidaceae (ASV11) and Limivicinus (ASV15) were more abundant in wheat. Monensin affected rumen microbial composition at a specific time. Transportation to feedlot significantly influenced microbiome structure and diversity in hay-fed calves. Bacterial taxa associated with body weight were classified, and core microbiotas interacted with each other during the trial.
CONCLUSIONS
In summary, the temporal dynamics of the rumen microbiome in cattle at the stocker and finishing stage are influenced by multiple factors of the feeding strategy. Diet at the stocker phase may temporarily affect the microbial composition during this stage. Modulating the rumen microbiome in the steers at the stocker stage affects the microbial interactions and performance in the finishing stage.
PubMed: 38273357
DOI: 10.1186/s40104-023-00967-5 -
Frontiers in Microbiology 2023Spontaneous fermentation of raw cow milk without backslopping is in practice worldwide as part of the traditional food culture, including "" preparation in earthen pots...
INTRODUCTION
Spontaneous fermentation of raw cow milk without backslopping is in practice worldwide as part of the traditional food culture, including "" preparation in earthen pots in Northeast India, "" of Niger and "" of Benin prepared in calabash vessels in West Africa. Very few reports are available about the differences in bacterial communities that evolved during the spontaneous mesophilic fermentation of cow milk in diverse geographical regions.
METHODS
In this study, we used high throughput amplicon sequencing of bacterial 16S rRNA gene to investigate 44 samples of naturally fermented homemade milk products and compared the bacterial community structure of these foods, which are widely consumed in Northeast India and Western Africa.
RESULTS AND DISCUSSION
The spontaneous milk fermentation shared the lactic acid bacteria, mainly belonging to and in these two geographically isolated regions. Indian samples showed a high bacterial diversity with the predominance of and , whereas was abundant in the West African samples. However, the cheese of Benin, prepared by curdling the milk with proteolytic leaf extract of followed by natural fermentation, contained spp.) as the dominant bacteria. Our analysis also detected several potential pathogens, like an emerging infectious foodborne pathogen in samples, an uncultured bacterium of in and samples, and spp. in the samples of Northeast India. These findings will allow us to develop strategies to address the safety issues related to spontaneous milk fermentation and implement technological interventions for controlled milk fermentation by designing starter culture consortiums for the sustainable production of uniform quality products with desirable functional and organoleptic properties.
PubMed: 37886068
DOI: 10.3389/fmicb.2023.1166518 -
Foods (Basel, Switzerland) Sep 2023High-throughput DNA sequencing (HTS) was used to study the microbial diversity of commercial traditional Izmir Tulum (IT) and Izmir Brined Tulum (IBT) cheeses from...
High-throughput DNA sequencing (HTS) was used to study the microbial diversity of commercial traditional Izmir Tulum (IT) and Izmir Brined Tulum (IBT) cheeses from Izmir, Türkiye. Simultaneously, cultivation-dependent methods were used to isolate, identify and characterize bacterial strains displaying probiotic potential. At the phylum level, dominated the microbiota of both cheese types comprising >98% of the population. Thirty genera were observed, with being the most abundant genus and with and subsp. being the most abundant species. Genera, including and , not previously associated with IT and IBT, were detected. IT cheeses displayed higher operational taxonomic units (OTUs; Richness) and diversity index (Simpson) than IBT cheeses; however, the difference between the diversity of the microbiota of IT and IBT cheese samples was not significant. Three strains isolated from IBT cheeses exhibited probiotic characteristics, which included capacity to survive under in vitro simulated gastrointestinal conditions, resistance to bile salts and potential to adhere to HT-29 human intestinal cells. These findings demonstrate that Tulum cheeses harbor bacterial genera not previously reported in this cheese and that some strains display probiotic characteristics.
PubMed: 37761191
DOI: 10.3390/foods12183482 -
Antibiotics (Basel, Switzerland) May 2023Antimicrobial resistance (AMR) is one of the biggest threats to public health. The food chain has been recognised as a vehicle for transmitting AMR bacteria. However,...
BACKGROUND
Antimicrobial resistance (AMR) is one of the biggest threats to public health. The food chain has been recognised as a vehicle for transmitting AMR bacteria. However, information about resistant strains isolated from African traditional fermented foods remains limited. is a traditional, naturally fermented milk product consumed by many pastoral communities across West Africa. The main aim of this study was to investigate and determine the AMR patterns of lactic acid bacteria (LAB) involved in the traditional fermentation of milk for production, and the presence of transferable AMR determinants.
METHODS
One hundred (100) LAB isolates from identified in a previous study as , , , , , and were investigated. The minimum inhibitory concentration (MIC) was determined for 18 antimicrobials using the micro-broth dilution method. In addition, LAB isolates were screened for 28 antimicrobial resistance genes using PCR. The ability of LAB isolates to transfer tetracycline and streptomycin resistance genes to was also investigated.
RESULTS
The experiments revealed variable antimicrobial susceptibility according to the LAB isolate and the antimicrobial tested. The tetracycline resistance genes (S) and (M) were detected in isolates 52 and 10. Additionally, (E) encoding resistance to streptomycin was detected in 52. The conjugation experiments suggested that the (S) and (E) genes were transferable in vitro from isolate 52 to JH2-2.
SIGNIFICANCE AND IMPACT
Traditional fermented foods play a significant role in the diet of millions of people in Africa, yet their contribution to the burden of AMR is largely unknown. This study highlights that LAB involved in traditionally fermented foods could be potential reservoirs of AMR. It also underscores the relevant safety issues of 52 and 10 for use as starter cultures as they carry transferable AMR genes. Starter cultures are an essential aspect of improving the safety and quality attributes of African fermented foods. However, AMR monitoring is an important safety aspect in the selection of starter cultures for improving traditional fermentation technologies.
PubMed: 37237746
DOI: 10.3390/antibiotics12050843 -
Anais Da Academia Brasileira de Ciencias 2022This study aims to evaluate the in silico genomic characteristics of Streptococcus infantarius subsp. infantarius, isolated from Coalho cheese from Paraíba, Brazil,...
This study aims to evaluate the in silico genomic characteristics of Streptococcus infantarius subsp. infantarius, isolated from Coalho cheese from Paraíba, Brazil, with a view to application in lactic fermentations. rRNA sequences from the 16S ribosomal region were used as input to GenBank, in the search for patterns that could reveal a non-pathogenic behavior of S. infantarius subsp. infantarius, comparing mobile genetic elements, antibiotic resistance genes, pan-genome analysis and multi-genome alignment among related species. S. infantarius subsp. infantarius CJ18 was the only complete genome reported by BLAST/NCBI with high similarity and after comparative genetics with complete genomes of Streptococcus agalactiae (SAG153, NJ1606) and Streptococcus thermophilus (ST106, CS18, IDCC2201, APC151) revealed that CJ18 showed a low number of transposases and integrases, infection by phage bacteria of the Streptococcus genus, absence of antibiotic resistance genes and presence of bacteriocin, folate and riboflavin producing genes. The genome alignment revealed that the collinear blocks of S. thermophilus ST106 and S. agalactiae SAG153 have inverted blocks when compared to the CJ18 genome due to gene positioning, insertions and deletions. Therefore, the strains of S. infantarius subsp. infantarius isolated from Coalho cheese from Paraíba showed genomic similarity with CJ18 and the mobility of genes analyzed in silico showed absence of pathogenicity throughout the genome of CJ18, indicating the potential of these strains for the dairy industry.
Topics: Fermentation; Streptococcus; Genomics; Sequence Analysis, DNA
PubMed: 36417612
DOI: 10.1590/0001-3765202220211447 -
Brazilian Journal of Microbiology :... Jun 2021The aim of this research was to identify the key lactic acid bacteria associated with the fermentation of dairy traditional fermented products for developing starter...
The aim of this research was to identify the key lactic acid bacteria associated with the fermentation of dairy traditional fermented products for developing starter cultures for controlled fermentation. A total of 100 lactic acid bacteria (LAB) were isolated from dairy traditional fermented products. Samples were obtained from eight producers in the South East of Nigeria. Isolates were identified by phenotypic and genotypic techniques including rep-PCR genotyping and sequencing of the 16S rRNA, pheS and rpoA genes. Isolates were characterised for antimicrobial activity against foodborne pathogens, exopolysaccharide (EPS) production and survival at low pH and in the presence of bile salts. All isolates clustered into 11 distinct rep-PCR groups and were identified as Lactobacillus fermentum (40%), Lactobacillus delbrueckii (23%), Streptococcus thermophilus (22%), Streptococcus infantarius (10%), Lactobacillus senioris (2%), Leuconostoc pseudomesenteriodes (2%) and Enterococcus thailandicus (1%). Lactobacillus fermentum showed a broad spectrum antimicrobial activity and survival at low pH, while Lactobacillus delbrueckii was able to tolerate low pH and produce EPS. All isolates survived in vitro exposure to 1% (w/v) bile salts over a 3-h period. L. fermentum, L. delbrueckii and S. thermophilus could be used to simulate the fermentation of dairy traditional fermented products.
Topics: Antibiosis; Bile Acids and Salts; Cultured Milk Products; Fermentation; Genes, Bacterial; Genotype; Hydrogen-Ion Concentration; Lactobacillales; Microbial Viability; Nigeria; Polysaccharides, Bacterial; RNA, Ribosomal, 16S
PubMed: 33694058
DOI: 10.1007/s42770-021-00461-y -
PloS One 2020The Streptococcus bovis/Streptococcus equinus complex (SBSEC) and possibly Streptococcus infantarius subsp. infantarius (Sii) are associated with human and animal...
The Streptococcus bovis/Streptococcus equinus complex (SBSEC) and possibly Streptococcus infantarius subsp. infantarius (Sii) are associated with human and animal diseases. Sii predominate in spontaneously fermented milk products with unknown public health effects. Sii/SBSEC prevalence data from West Africa in correlation with milk transformation practices are limited. Northern Côte d'Ivoire served as study area due to its importance in milk production and consumption and to link a wider Sudano-Sahelian pastoral zone of cross-border trade. We aimed to describe the cow milk value chain and determine Sii/SBSEC prevalence with a cross-sectional study. Dairy production practices were described as non-compliant with basic hygiene standards. The system is influenced by secular sociocultural practices and environmental conditions affecting product properties. Phenotypic and molecular analyses identified SBSEC in 27/43 (62.8%) fermented and 26/67 (38.8%) unfermented milk samples. Stratified by collection stage, fermented milk at producer and vendor levels featured highest SBSEC prevalence of 71.4% and 63.6%, respectively. Sii with 62.8% and 38.8% as well as Streptococcus gallolyticus subsp. macedonicus with 7.0% and 7.5% were the predominant SBSEC species identified among fermented and unfermented milk samples, respectively. The population structure of Sii/SBSEC isolates seems to reflect evolving novel dairy-adapted, non-adapted and potentially pathogenic lineages. Northern Côte d'Ivoire was confirmed as area with high Sii presence in dairy products. The observed production practices and the high diversity of Sii/SBSEC supports in-depth investigations on Sii ecology niche, product safety and related technology in the dairy value chain potentially affecting large population groups across sub-Saharan Africa.
Topics: Animals; Cattle; Cote d'Ivoire; Cross-Sectional Studies; Cultured Milk Products; Female; Food Microbiology; Humans; Milk; Phylogeny; Streptococcus; Streptococcus bovis; Streptococcus gallolyticus
PubMed: 32413097
DOI: 10.1371/journal.pone.0233132 -
PloS One 2020Streptococcus pneumoniae infections are one of the major causes of morbility and mortality worldwide. Although vaccination and antibiotherapy constitute fundamental and...
Streptococcus pneumoniae infections are one of the major causes of morbility and mortality worldwide. Although vaccination and antibiotherapy constitute fundamental and complementary strategies against pneumococcal infections, they present some limitations including the increase in non-vaccine serotypes and the emergence of multidrug-resistances, respectively. Ribosomally-synthesized antimicrobial peptides (i.e. bacteriocins) produced by Lactic Acid Bacteria (LAB) may represent an alternative or complementary strategy to antibiotics for the control of pneumococal infections. We tested the antimicrobial activity of 37 bacteriocinogenic LAB, isolated from food and other sources, against clinical S. pneumoniae strains. Streptococcus infantarius subsp. infantarius LP90, isolated from Venezuelan water-buffalo milk, was selected because of its broad and strong anti-pneumococcal spectrum. The in vitro safety assessment of S. infantarius LP90 revealed that it may be considered avirulent. The analysis of a 19,539-bp cluster showed the presence of 29 putative open reading frames (ORFs), including the genes encoding 8 new class II-bacteriocins, as well as the proteins involved in their secretion, immunity and regulation. Transcriptional analyses evidenced that the induction factor (IF) structural gene, the bacteriocin/IF transporter genes, the bacteriocin structural genes and most of the bacteriocin immunity genes were transcribed. MALDI-TOF analyses of peptides purified using different multichromatographic procedures revealed that the dairy strain S. infantarius LP90 produces at least 6 bacteriocins, including infantaricin A1, a novel anti-pneumococcal two-peptide bacteriocin.
Topics: Amino Acid Sequence; Anti-Bacterial Agents; Bacteriocins; Humans; Pneumococcal Infections; Streptococcus
PubMed: 32134941
DOI: 10.1371/journal.pone.0229417 -
PloS One 2019Streptococcus infantarius subsp. infantarius (Sii) has been identified as predominant lactic acid bacteria in spontaneously fermented dairy products (FDPs) in...
Streptococcus infantarius subsp. infantarius (Sii) has been identified as predominant lactic acid bacteria in spontaneously fermented dairy products (FDPs) in sub-Saharan Africa including Côte d'Ivoire. However, Sii belongs to the Streptococcus bovis/Streptococcus equinus complex (SBSEC). Most SBSEC members are assumed to be involved as opportunistic pathogens in serious diseases in both humans and animals. A population-based cross-sectional survey, including 385 participants was conducted in Korhogo, northern Côte d'Ivoire, to identify risk factors for Sii fecal carriage, including consumption of local FDPs. A structured questionnaire was used to gather participant's socio-demographic and economic characteristics, their relation to livestock and dietary habits. In addition, fresh stool and milk samples were collected. The identification of Sii was done using a SBSEC-specific PCR assay targeting 16S rRNA and groEL genes. The overall prevalence of SBSEC and Sii carriage was 23.2% (confidence interval CI 95% = 18.9-27.5) and 12.0% (CI 95% = 8.4-15.5) for stool, respectively. Prevalence of Sii was significantly higher in consumers of artisanal butter compared with non-consumers (57.1% vs 10.1%, odds ratio OR: 11.9, 95% CI: 3.9-36.6), as well as in persons handling livestock (OR = 3.9; 95% CI = 1.6-9.3) and livestock primary products (OR = 5.7; 95% CI = 2.3-14.3). The closer contact with livestock was a risk factor for Sii fecal carriage. Sii strains were isolated from fresh and fermented milk products with a prevalence of 30.4% and 45.4%, respectively. Analysis of Sii population structure through the SBSEC multi locus sequence typing assay revealed a close relationship across human and dairy isolates, possibly linked to a Kenyan human isolate. All these outcomes underline the interest of in-depth investigations on the ecology, potential reservoirs and pathways of contamination by Sii at the human-animal-environment interface in comparison to yet to be collected data from Europe, Asia and the Americas to further elucidate the various roles of Sii.
Topics: Adolescent; Adult; Animals; Cross-Sectional Studies; Cultured Milk Products; Feces; Female; Food Microbiology; Gram-Positive Bacterial Infections; Humans; Kenya; Male; Middle Aged; Milk; Multilocus Sequence Typing; RNA, Ribosomal, 16S; Risk Factors; Streptococcus; Young Adult
PubMed: 31774832
DOI: 10.1371/journal.pone.0225452 -
Frontiers in Microbiology 2018ssp. 25124 (25124) is a lactic acid bacterium (LAB) isolated from , a refreshing beverage prepared by suspending fermented (a thermal and alkali-treated maize dough)...
ssp. 25124 (25124) is a lactic acid bacterium (LAB) isolated from , a refreshing beverage prepared by suspending fermented (a thermal and alkali-treated maize dough) in water. Although s are the predominant strains in fermented doughs, such as sourdoughs, and non-nixtamalized fermented maize foods, the microbiota is markedly different. This may be the result of the nixtamalization process, which could act as a selective force of some strains. 25124 has been reported as the main amylolytic LAB in pozol; starch is the primary carbon source on since monosaccharides and disaccharides are lost during nixtamalization; however, non-amylolytic LAB counts are higher than amylolytic LAB in after 24-h fermentation suggesting that another carbon source is being used by the former bacteria. Hemicellulose (arabinoxylan in maize) becomes available via nixtamalization and is subsequently metabolized by LAB. The aim of this work was to determine whether this bacterium is able to use arabinoxylan as the only carbon source in a defined medium containing arabinoxylan extracted from either (wash water produced during preparation), or beechwood xylan. Xylanase activity in the presence of arabinoxylan (135.8 ± 48.7 IU/mg protein) was higher than that of beechwood (62.5 ± 19.8 IU/mg protein). Other enzymatic activities, such as arabinofuranosidase and acetyl esterase, were also detected, suggesting the adaptation of the bacterium studied to dough. It was concluded that 25124 isolated from was able to use arabinoxylans, which are present in nixtamal dough, so fermentation does not depend exclusively on free sugars and starch.
PubMed: 30619147
DOI: 10.3389/fmicb.2018.03061