Specificity of the AMP-6000 Method for Enumerating Clostridium Endospores in Milk

Enumeration of endospores of butyric acid-forming clostridia in cheese milk is an essential part of milk quality monitoring for cheese producers to avoid late blowing, severe spoilage caused by clostridia during ripening. However, due to the lack of an internationally standardized method, different methods are used and it is important to consider how the choice of method affects the results. This is particularly relevant when clostridial spore counts in milk are considered for quality payments. The aim of this study was to evaluate the specificity of the AMP-6000 method for the enumeration of endospores of cheese spoiling clostridia in milk. First, to assess the prevalence of Clostridium diversity and to determine potential non-target species, we identified isolates from positive reactions of the AMP-6000 method used to quantify clostridial endospores in raw milk and teat skin samples by MALDI-TOF MS. Based on these results, a strain library was designed to evaluate method inclusivity and exclusivity using pure cultures of target and non-target strains according to ISO 16140-2:2016. Most target Clostridium tyrobutyricum strains, as well as all tested C. butyricum and C. sporogenes strains were inclusive. However, C. beijerinckii may be underestimated as only some strains gave positive results. All non-target strains of bacilli and lysinibacilli, but not all paenibacilli, were confirmed to be exclusive. This study provides performance data to better understand the results of microbiological enumeration of butyric acid-forming clostridia in milk and serves as a basis for future methodological considerations and improvements.

Clostridium strain FAM25158, a unique endospore-forming bacterium related to Clostridium tyrobutyricum and isolated from Emmental cheese shows low tolerance to salt

The genus Clostridium is a large and diverse group of species that can cause food spoilage, including late blowing defect (LBD) in cheese. In this study, we investigated the taxonomic status of strain FAM25158 isolated from Emmental cheese with LBD using a polyphasic taxonomic and comparative genomic approach. A 16S rRNA gene sequence phylogeny suggested affiliation to the Clostridium sensu stricto cluster, with Clostridium tyrobutyricum DSM 2637T being the closest related type strain (99.16% sequence similarity). Average Nucleotide Identity (ANI) analysis revealed that strain FAM25158 is at the species threshold with C. tyrobutyricum, with ANI values ranging from 94.70 to 95.26%, while the digital DNA-DNA hybridization values were below the recommended threshold, suggesting that FAM25158 is significantly different from C. tyrobutyricum at the genomic level. Moreover, comparative genomic analysis between FAM25158 and its four closest C. tyrobutyricum relatives revealed a diversity of metabolic pathways, with FAM25158 differing from other C. tyrobutyricum strains by the presence of genes such as scrA, srcB, and scrK, responsible for sucrose utilization, and the absence of many important functional genes associated with cold and osmolality adaptation, which was further supported by phenotypic analyses. Surprisingly, strain FAM25158 exhibited unique physiologic traits, such as an optimal growth temperature of 30°C, in contrast to its closest relatives, C. tyrobutyricum species with an optimal growth temperature of 37°C. Additionally, the growth of FAM25158 was inhibited at NaCl concentrations higher than 0.5%, a remarkable observation considering its origin from cheese. While the results of this study provide novel information on the genetic content of strain FAM25158, the relationship between its genetic content and the observed phenotype remains a topic requiring further investigation.

Importance of Pre-Milking Udder Hygiene to Reduce Transfer of Clostridial Spores from Teat Skin to Raw Milk

Butyric acid producing clostridia (BAPC) cause the so-called late-blowing defect, a serious quality problem in semi-hard and hard cheeses. Late-blown cheeses are characterized by undesired slits and cracks, irregular eyes, and off-flavors due to excessive amounts of gas and organic acids produced by clostridia. Clostridial transfer to raw milk can occur during milking through dirty teats. Therefore, teat cleaning before milking is a key factor in preventing clostridial contamination of the milk. However, different cleaning methods are used, and little information is available on the efficacy of routine teat cleaning in reducing clostridial endospores. The main objectives of this study were to assess the extent of udder contamination with BAPC spores and to investigate the efficacy of routine teat cleaning on BAPC spore counts in milk. In a longitudinal study, eight dairy farms were visited during five sampling events. Clostridial spore counts were quantified from teat skin before and after routine teat cleaning, in pooled quarter milk samples from individual cows, and in bulk tank milk samples using a most probable number method. In addition, farm management data were collected periodically through a survey, and average cow cleanliness was assessed by a veterinarian. On average, teat cleaning resulted in a 0.6 log unit reduction in BAPC spores on teat skin, and a strong positive correlation was found between BAPC spore concentrations on teat skin after cleaning and in pooled quarter milk samples. Seasonal variations and the potential influence of differences in farm management were also noted. Interestingly, average cow cleanliness correlated strongly with BAPC spore levels in milk, suggesting the potential for a quick and rough estimation method of clostridial contamination that could be implemented by farmers.

Comparative Genomics Provides Insights Into Genetic Diversity of Clostridium tyrobutyricum and Potential Implications for Late Blowing Defects in Cheese

Clostridium tyrobutyricum has been recognized as the main cause of late blowing defects (LBD) in cheese leading to considerable economic losses for the dairy industry. Although differences in spoilage ability among strains of this species have been acknowledged, potential links to the genetic diversity and functional traits remain unknown. In the present study, we aimed to investigate and characterize genomic variation, pan-genomic diversity and key traits of C. tyrobutyricum by comparing the genomes of 28 strains. A comparative genomics analysis revealed an “open” pangenome comprising 9,748 genes and a core genome of 1,179 genes shared by all test strains. Among those core genes, the majority of genes encode proteins related to translation, ribosomal structure and biogenesis, energy production and conversion, and amino acid metabolism. A large part of the accessory genome is composed of sets of unique, strain-specific genes ranging from about 5 to more than 980 genes. Furthermore, functional analysis revealed several strain-specific genes related to replication, recombination and repair, cell wall, membrane and envelope biogenesis, and defense mechanisms that might facilitate survival under stressful environmental conditions. Phylogenomic analysis divided strains into two clades: clade I contained human, mud, and silage isolates, whereas clade II comprised cheese and milk isolates. Notably, these two groups of isolates showed differences in certain hypothetical proteins, transcriptional regulators and ABC transporters involved in resistance to oxidative stress. To the best of our knowledge, this is the first study to provide comparative genomics of C. tyrobutyricum strains related to LBD. Importantly, the findings presented in this study highlight the broad genetic diversity of C. tyrobutyricum, which might help us understand the diversity in spoilage potential of C. tyrobutyricum in cheese and provide some clues for further exploring the gene modules responsible for the spoilage ability of this species.

Storage media and RNA extraction approaches substantially influence the recovery and integrity of livestock fecal microbial RNA

Background

There is growing interest in understanding gut microbiome dynamics, to increase the sustainability of livestock production systems and to better understand the dynamics that regulate antibiotic resistance genes (i.e., the resistome). High-throughput sequencing of RNA transcripts (RNA-seq) from microbial communities (metatranscriptome) allows an unprecedented opportunity to analyze the functional and taxonomical dynamics of the expressed microbiome and emerges as a highly informative approach. However, the isolation and preservation of high-quality RNA from livestock fecal samples remains highly challenging. This study aimed to determine the impact of the various sample storage and RNA extraction strategies on the recovery and integrity of microbial RNA extracted from selected livestock (chicken and pig) fecal samples.

Methods

Fecal samples from pigs and chicken were collected from conventional slaughterhouses. Two different storage buffers were used at two different storage temperatures. The extraction of total RNA was done using four different commercially available kits and RNA integrity/quality and concentration were measured using a Bioanalyzer 2100 system with RNA 6000 Nano kit (Agilent, Santa Clara, CA, USA). In addition, RT-qPCR was used to assess bacterial RNA quality and the level of host RNA contamination.

Results

The quantity and quality of RNA differed by sample type (i.e., either pig or chicken) and most significantly by the extraction kit, with differences in the extraction method resulting in the least variability in pig feces samples and the most variability in chicken feces. Considering a tradeoff between the RNA yield and the RNA integrity and at the same time minimizing the amount of host RNA in the sample, a combination of storing the fecal samples in RNALater at either 4 °C (for 24 h) or -80 °C (up to 2 weeks) with extraction with PM kit (RNEasy Power Microbiome Kit) had the best performance for both chicken and pig samples.

Conclusion

Our findings provided a further emphasis on using a consistent methodology for sample storage, duration as well as a compatible RNA extraction approach. This is crucial as the impact of these technical steps can be potentially large compared with the real biological variability to be explained in microbiome and resistome studies.

Irradiated Non-replicative Lactic Acid Bacteria Preserve Metabolic Activity While Exhibiting Diverse Immune Modulation

In the recent years, safety concerns regarding the administration of probiotics led to an increased interest in developing inactivated probiotics, also called “paraprobiotics”. Gamma irradiation represents a promising tool that can be used to produce safe paraprobiotics by inhibiting replication while preserving the structure, the metabolic activity, and the immunogenicity of bacteria. In this study, we evaluated the ability of four strains of lactic acid bacteria (LAB: Lacticaseibacillus casei, Lactobacillus acidophilus, Lactiplantibacillus plantarum, and Lacticaseibacillus paracasei) in preserving the metabolic activity and the immune modulation of swine porcine peripheral blood mononuclear cells, after gamma irradiation or heat inactivation. Our results show that all four strains retained the metabolic activity following gamma irradiation but not after heat inactivation. In terms of immune-modulatory capacity, irradiated L. acidophilus and Lc. paracasei were able to maintain an overall gene expression pattern similar to their live state, as heat inactivation did with Lc. casei. Moreover, we show that the two inactivation methods applied to the same strain can induce an opposed expression of key genes involved in pro-inflammatory response (e.g., IFNα and interleukin-6 for Lc. casei), whereas gamma irradiation of L. acidophilus and Lc. paracasei was able to induce a downregulation of the anti-inflammatory TGFβ. Taken together, our data show that immune modulation can be impacted not only by different inactivation methods but also by the strain of LAB selected. This study highlights that gamma irradiation harbors the potential to produce safe non-replicative metabolically active LAB and identifies immunomodulatory capacities that may be applied as vaccine adjuvants.

Metatranscriptomic Analysis of the Chicken Gut Resistome Response to In-Feed Antibiotics and Natural Feed Additives

The emergence of resistance against common antibiotics in the gut microbiota is a major issue for both human and livestock health. This highlights the need for understanding the impact of such application on the reservoir of antibiotic resistance genes in poultry gut and devising means to circumvent the potential resistome expansion. Phytogenic feed additives (PFAs) are potential natural alternative to antibiotic to improve animal health and performance, supposedly via positively affecting the gut microbial ecosystem, but there is little systematic information available. In this time-course study, we applied a shotgun meta-transcriptomics approach to investigate the impact of a PFA product as well as the commonly used antibiotic, zinc bacitracin either at AGP concentration or therapeutic concentration on the gut microbiome and resistome of broiler chickens raised for 35 days. Over the course of the trial, PFA treatments increased the abundance of Firmicutes such as Lactobacillus and resulted in a lower abundance of Escherichia, while the latter group increased significantly in the feces of chickens that received either AGP or AB doses of bacitracin. Tetracycline resistance and aminoglycoside resistance were the predominant antibiotic resistance gene (ARG) classes found, regardless of the treatment. PFA application resulted in a decrease in abundance of ARGs compared to those in the control group and other antibiotic treatment groups. In summary, the findings from this study demonstrate the potential of phytogenic feed additives could be an alternative to antibiotics in poultry farming, with the added benefit of counteracting antimicrobial resistance development.

Effect of Two Soybean Varieties Treated with Different Heat Intensities on Ileal and Caecal Microbiota in Broiler Chickens

Simple Summary

Soybeans are an essential part of today’s poultry nutrition diets because of their high protein content and quality. To ensure optimum digestibility in monogastric animals, soybeans need to be thermally processed. As required heat intensities depend on individual soybean properties, the emergence of highly heterogenic soybean batches is a challenge for adequate processing conditions. Molecular changes occurring during heat treatment can alter the microbial communities colonizing the animals’ guts. Gut microbiota is of great importance for both its host animal’s performance and health. To investigate the effect of heat treatment and soybean variety on the chickens’ microbiota, two soybean varieties were selected, treated at two different heat intensities and subjected to a feeding trial. DNA was then extracted and sequenced to identify different bacterial populations in the digesta of certain gut sections. Results showed that both the soybean variety and the applied heat treatment affected the abundance of certain bacterial species in the gut of chickens, but no effect on the taxonomy level of family or genus appeared. This underlines the sensitivity and reactivity of the highly complex microbial community to apparently small dietary differences.

Abstract

Soybean products are of high importance for the protein supply of poultry. Heat treatment of soybeans is essential to ensure optimal digestibility because of intrinsic antinutritive factors typical for this feed category. However, excessive treatment promotes the Maillard reaction and reduces protein digestibility. Furthermore, Europe’s efforts are to decrease dependence on imports of soybean products and enlarge local production. This process will include an increase in the variability of soybean batches, posing great challenges to adequate processing conditions. Intrinsic soybean properties plus heat treatment intensity might be able to modulate the gut microbiota, which is of crucial importance for an animal’s health and performance. To assess the influence of heat treatment and soybean variety on gut microbiota, 2 soybean cakes from 2 varieties were processed at 110 °C or 120 °C and subsequently fed to 336 one-day-old broiler chickens. After 36 days, the animals were slaughtered, and the digesta of the ileum and caecum was collected. Next, 16S rRNA amplicon sequencing of the extracted DNA revealed a high discrepancy between gut sections, but there were no differences between male and female birds. Significant differences attributed to the different soybean varieties and heat intensity were detected for certain bacterial taxa. However, no effect on specific families or genera appeared. In conclusion, the results indicated the potential of processing conditions and soybean variety as microbiota-modulating factors.

The gut bacterial microbiome of Nile tilapia (Oreochromis niloticus) from lakes across an altitudinal gradient

Background

Microorganisms inhabiting the gut play a significant role in supporting fundamental physiological processes of the host, which contributes to their survival in varied environments. Several studies have shown that altitude affects the composition and diversity of intestinal microbial communities in terrestrial animals. However, little is known about the impact of altitude on the gut microbiota of aquatic animals. The current study examined the variations in the gut microbiota of Nile tilapia (Oreochromis niloticus) from four lakes along an altitudinal gradient in Ethiopia by using 16S rDNA Illumina MiSeq high-throughput sequencing.

Results

The results indicated that low-altitude samples typically displayed greater alpha diversity. The results of principal coordinate analysis (PCoA) showed significant differences across samples from different lakes. Firmicutes was the most abundant phylum in the Lake Awassa and Lake Chamo samples whereas Fusobacteriota was the dominant phylum in samples from Lake Hashengie and Lake Tana. The ratio of Firmicutes to Bacteroidota in the high-altitude sample (Lake Hashengie, altitude 2440 m) was much higher than the ratio of Firmicutes to Bacteroidota in the low altitude population (Lake Chamo, altitude 1235 m). We found that the relative abundances of Actinobacteriota, Chloroflexi, Cyanobacteria, and Firmicutes were negatively correlated with altitude, while Fusobacteriota showed a positive association with altitude. Despite variability in the abundance of the gut microbiota across the lakes, some shared bacterial communities were detected.

Conclusions

In summary, this study showed the indirect influence of altitude on gut microbiota. Altitude has the potential to modulate the gut microbiota composition and diversity of Nile tilapia. Future work will be needed to elucidate the functional significance of gut microbiota variations based on the geographical environment.

Significance and impact of the study

Our study determined the composition and diversity of the gut microbiota in Nile tilapia collected from lakes across an altitude gradient. Our findings greatly extend the baseline knowledge of fish gut microbiota in Ethiopian lakes that plays an important role in this species sustainable aquaculture activities and conservation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02496-z.

Propionic acid bacteria in the food industry: An update on essential traits and detection methods

Propionic acid bacteria (PAB) is an umbrella term for a group of bacteria with the ability to produce propionic acid. In the past, due to this common feature and other phenotypic similarities, genetically heterogeneous bacteria were considered as a single genus, Propionibacterium. Members of this genus ranged from "dairy propionibacteria," which are widely known for their role in eye and flavor formation in cheese production, to "cutaneous propionibacteria," which are primarily associated with human skin. In 2016, the introduction of two new genera based on genotypic data facilitated a clear separation of cutaneous (Cutibacterium spp.) from dairy PAB (Propionibacterium spp., Acidipropionibacterium spp.). In light of these taxonomic changes, but with particular emphasis on dairy PAB, this review describes the current state of knowledge about metabolic pathways and other characteristics such as antibiotic resistance and virulence factors. In addition, the relevance of dairy PAB for the food industry and cheese production in particular is highlighted. Furthermore, methods for cultivation, detection, and enumeration are reviewed, incorporating the current taxonomy as well as the potential for routine applications.

Biofilm-Forming Ability of Microbacterium lacticum and Staphylococcus capitis Considering Physicochemical and Topographical Surface Properties

Biofilm characteristics of Microbacterium lacticum D84 (M. lacticum) and Staphylococcus capitis subsp. capitis (S. capitis) on polytetrafluoroethylene and AISI-304 stainless steel at early- (24, 48 h) and late-stage (144, 192 h) biofilm formation were investigated. M. lacticum biofilm structure was more developed compared to S. capitis, representing vastly mature biofilms with a strongly developed amorphous matrix, possibly extracellular polymeric substances (EPSs), at late-stage biofilm formation. S. capitis showed faster growth behavior but still resulted in a relatively flat biofilm structure. Strong correlations were found between several roughness parameters and S. capitis surface coverage (r ≥ 0.98), and between total surface free energy (γs) and S. capitis surface coverage (r = 0.89), while M. lacticum remained mostly unaffected. The pronounced ubiquitous biofilm characteristics make M. lacticum D84 a suitable model for biofilm research. Studying biofilm formation of these bacteria may help one understand bacterial adhesion on interfaces and hence reduce biofilm formation in the food industry.

The Impact of Sampling Season and Catching Site (Wild and Aquaculture) on Gut Microbiota Composition and Diversity of Nile Tilapia (Oreochromis niloticus)

Simple Summary

The gut microbiota (all microbes in the intestine) of fishes is known to play an essential role in diverse aspects of their life. The gut microbiota of fish is affected by various environmental parameters, including temperature changes, salinity and diet. This study characterised the microbial composition in gut samples of Nile Tilapia collected from Lake Tana and the Bahir Dar aquaculture facility centre applying modern molecular techniques. The results show clear differences in the gut microbiota in fish from the Lake Tana and the ones from aquaculture. Further, also significant differences were observed on the composition of the gut microbiota across sampling months. Samples from the aquaculture centre displayed a higher diversity than the wild catch Nile tilapia from Lake Tana even though there is also an overlapping of the detected microbial groups. Overall, this is the first study on the effects of sampling season and catching site on the gut microbiota of Nile tilapia in Ethiopia. Future work will help to precisely explain the causes of these changes and their influence of the health and growth of Nile tilapia in Ethiopian lakes as well as under aquaculture conditions.

Abstract

The gut microbiota of fishes is known to play an essential role in diverse aspects of host biology. The gut microbiota of fish is affected by various environmental parameters, including temperature changes, salinity and diet. Studies of effect of environment on gut microbiota enables to have a further understanding of what comprises a healthy microbiota under different environmental conditions. However, there is insufficient understanding regarding the effects of sampling season and catching site (wild and aquaculture) on the gut microbiota of Nile tilapia. This study characterised gut microbial composition and diversity from samples collected from Lake Tana and the Bahir Dar aquaculture facility centre using 16S rDNA Illumina MiSeq platform sequencing. Firmicutes and Fusobacteria were the most dominant phyla in the Lake Tana samples, while Proteobacteria was the most dominant in the aquaculture samples. The results of differential abundance testing clearly indicated significant differences for Firmicutes, Fusobacteria, Bacteroidetes and Cyanobacteria across sampling months. However, Proteobacteria, Chloroflexi, Fusobacteria and Cyanobacteria were significantly enriched in the comparison of samples from the Lake Tana and aquaculture centre. Significant differences were observed in microbial diversity across sampling months and between wild and captive Nile tilapia. The alpha diversity clearly showed that samples from the aquaculture centre (captive) had a higher diversity than the wild Nile tilapia samples from Lake Tana. The core gut microbiota of all samples of Nile tilapia used in our study comprised Firmicutes, Proteobacteria and Fusobacteria. This study clearly showed the impact of sampling season and catching site (wild and aquaculture) on the diversity and composition of bacterial communities associated with the gut of Nile tilapia. Overall, this is the first study on the effects of sampling season and catching site on the gut microbiota of Nile tilapia in Ethiopia. Future work is recommended to precisely explain the causes of these changes using large representative samples of Nile tilapia from different lakes and aquaculture farms.

Functional Properties and Sustainability Improvement of Sourdough Bread by Lactic Acid Bacteria

Preventing food spoilage without the addition of chemical food additives, while increasing functional properties of wheat-based bakery products, is an increasing demand by the consumers and a challenge for the food industry. Within this study, lactic acid bacteria (LAB) isolated from sourdough were screened in vitro for the ability to utilize the typical wheat carbohydrates, for their antimicrobial and functional properties. The dual culture overlay assay revealed varying levels of inhibition against the examined fungi, with Lactiplantibacillus plantarum S4.2 and Lentilactobacillusparabuchneri S2.9 exhibiting the highest suppression against the indicator strains Fusarium graminearum MUCL43764, Aspergillus fumigatus, A. flavus MUCL11945, A. brasiliensis DSM1988, and Penicillium roqueforti DSM1079. Furthermore, the antifungal activity was shown to be attributed mainly to the activity of acids produced by LAB. The antibacillus activity was evaluated by the spot-on-the-lawn method revealing a high inhibition potential of the majority of LAB isolated from sourdough against Bacillus cereus DSM31, B. licheniformis DSM13, B. subtilis LMG7135, and B. subtilis S15.20. Furthermore, evaluating the presence of the glutamate decarboxylase gen in LAB isolates by means of PCR showed a strain dependency of a potential GABA production. Finally, due to improved functional activities, LAB isolated from sourdoughs exhibit promising characteristics for the application as natural preservatives in wheat-based bakery products.

Strain-Dependent Cheese Spoilage Potential of Clostridium tyrobutyricum

Clostridium tyrobutyricum, a Gram-positive, anaerobic, spore-forming bacterium, is considered as one of the main causative agents for spoilage of hard and semihard cheeses. Growth of C. tyrobutyricum in cheese is critically influenced by ripening temperature and time, pH, salt and lactic acid concentration, moisture and fat content, and the presence of other microorganisms. Previous studies revealed high intraspecies diversity of C. tyrobutyricum strains and variable tolerance toward pH, temperatures, and salt concentrations. These findings indicate that strain-dependent characteristics may be relevant to assess the risk for cheese spoilage if clostridial contamination occurs. In this study, we aimed to compare the phenotypes of 12 C. tyrobutyricum strains which were selected from 157 strains on the basis of genotypic and proteotypic variability. The phenotypic analysis comprised the assessment of gas production and organic acid concentrations in an experimental cheese broth incubated at different temperatures (37, 20, and 14 °C). For all tested strains, delayed gas production at lower incubation temperatures and a strong correlation between gas production and the change in organic acid concentrations were observed. However, considering the time until gas production was visible at different incubation temperatures, a high degree of heterogeneity was found among the tested strains. In addition, variation among replicates of the same strain and differences due to different inoculum levels became evident. This study shows, that, among other factors, strain-specific germination and growth characteristics should be considered to evaluate the risk of cheese spoilage by C. tyrobutyricum.

Insights into the Potential of Sourdough-Related Lactic Acid Bacteria to Degrade Proteins in Wheat

Sourdough processing contributes to better digestible wheat-based bakery products, especially due to the proteolytic activity of lactic acid bacteria (LAB). Therefore, sourdough-related LAB were screened for their capacity to degrade immunogenic proteins like gluten and alpha-amylase-trypsin inhibitors (ATIs). Firstly, the growth of 87 isolates was evaluated on a gluten-based medium. Further, the breakdown capacity of selected isolates was determined for gluten with a focus on gliadins by measuring acidification parameters and MALDI-TOF MS protein profiles. ATI degradation after 72 h of incubation within an ATI-based medium was investigated by means of acidification, HPLC, and competitive ELISA. All isolates exhibited the potential to degrade ATIs to a high degree, whereas the gliadin degradation capacity varied more greatly among tested LAB, with Lacticaseibacillus paracasei Lpa4 exhibiting the strongest alterations of the gliadin pattern, followed by Lactiplantibacillus plantarum Lpl5. ATI degradation capacities ranged from 52.3% to 85.0% by HPLC and 22.2% to 70.2% by ELISA, with Lacticaseibacillus paracasei Lpa4 showing superior breakdown properties. Hence, a selection of specific starter cultures can be used in sourdough processing for wheat-based bakery products with reduced gluten and ATI content and, further, better tolerated products for patients suffering from non-celiac wheat sensitivity (NCWS).

Short-Chain Cello-oligosaccharides: Intensification and Scale-up of Their Enzymatic Production and Selective Growth Promotion among Probiotic Bacteria

Short-chain cello-oligosaccharides (COS; degree of polymerization, DP ≤ 6) are promising water-soluble dietary fibers. An efficient approach to their bottom-up synthesis is from sucrose and glucose using glycoside phosphorylases. Here, we show the intensification and scale up (20 mL; gram scale) of COS production to 93 g/L product and in 82 mol % yield from sucrose (0.5 M). The COS were comprised of DP 3 (33 wt %), DP 4 (34 wt %), DP 5 (24 wt %), and DP 6 (9 wt %) and involved minimal loss (≤10 mol %) to insoluble fractions. After isolation (≥95% purity; ≥90% yield), the COS were examined for growth promotion of probiotic strains. Benchmarked against inulin, trans-galacto-oligosaccharides, and cellobiose, COS showed up to 4.1-fold stimulation of cell density for Clostridium butyricum, Lactococcus lactis subsp. lactis, Lactobacillus paracasei subsp. paracasei, and Lactobacillus rhamnosus but were less efficient with Bifidobacterium sp. This study shows the COS as selectively functional carbohydrates with prebiotic potential and demonstrates their efficient enzymatic production.

Metabarcoding Analyses of Gut Microbiota of Nile Tilapia (Oreochromis niloticus) from Lake Awassa and Lake Chamo, Ethiopia

The Nile tilapia (Oreochromis niloticus) gut harbors a diverse microbial community; however, their variation across gut regions, lumen and mucosa is not fully elucidated. In this study, gut microbiota of all samples across gut regions and sample types (luminal content and mucosa) were analyzed and compared from two Ethiopian lakes. Microbiota were characterized using 16S rRNA Illumina MiSeq platform sequencing. A total of 2061 operational taxonomic units (OTUs) were obtained and the results indicated that Nile tilapia from Lake Chamo harbored a much more diversified gut microbiota than Lake Awassa. In addition, the gut microbiota diversity varied significantly across the gut region based on the Chao1, Shannon and Simpson index. The microbiome analyses of all samples in the midgut region showed significantly higher values for alpha diversity (Chao 1, Shannon and Simpson). Beta diversity analysis revealed a clear separation of samples according to sampling areas and gut regions. The most abundant genera were Clostridium_sensu_stricto and Clostridium_XI genera across all samples. Between the two sampling lakes, two phyla, Phylum Fusobacteria and Cyanobacteria, were found to be significantly different. On the other hand, six phyla (Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria and Cyanobacteria) were significantly different across gut regions. In this study, we found that all samples shared a large core microbiota, comprising a relatively large number of OTUs, which was dominated by Proteobacteria, Firmicutes, Cyanobacteria, Fusobacteria and Actinobacteria. This study has established the bases for future large-scale investigations of gut microbiota of fishes in Ethiopian lakes.

Bacterial growth dynamics and corresponding metabolite levels in the extraction area of an Austrian sugar beet factory using antimicrobial treatment

BACKGROUND

During the manufacture of sucrose from sugar beet, different microorganisms originating from the plant material as well as from the soil enter the process. Due to the formation of polysaccharide-based slimes, these contaminants may induce several adverse effects such as filtration problems during juice purification. Certain microorganisms also metabolize sucrose, leading to product losses with financial consequences. To better understand and to prevent these negative effects, the aim of the study was to investigate the evolution of relevant bacterial groups, including their metabolites appearing during the extraction process. For this purpose, one production cycle was monitored to identify the major contamination steps and to clarify how they relate to the processing conditions. Traditionally, different antimicrobial agents such as formaldehyde, sulfur dioxide, hypochlorous acid, sodium hypochlorite, and chlorine dioxide have been added to inhibit microbial growth. In the present study, a rosin-based product derived from pine trees was applied as an alternative to those substances.

RESULTS

Press water, raw juice, and mid-tower juice were identified as being highly contaminated with bacteria, and processing conditions such as time, temperature and pH level significantly influenced bacterial levels and the corresponding metabolites. Among the contaminants identified, lactic acid bacteria, and mesophilic and thermophilic aerobic bacteria played a dominant role, whereas lactic acid, acetic acid, butyric acid, and ethanol were identified as typical metabolites.

CONCLUSION

Bacterial growth during production could be reduced by shock dosing of the rosin-based material in the extraction area. © 2020 Society of Chemical Industry.

Biogenic Amine Contents and Microbial Characteristics of Cambodian Fermented Foods

Naturally fermented foods are an important part of the typical diet in Cambodia. However, the food safety status of these products has not been widely studied. The aim of this study was, therefore, to provide an overview of the quality of these foods in relation to microbiology and biogenic amines. Additionally, the obtained results were compared to the habits and practices of Cambodians in handling this type of food. A total of 57 fermented foods (42 fishery and 15 vegetable products) were collected from different retail markets in the capital of Cambodia. Pathogenic Salmonella spp., Listeria spp., and Listeria monocytogenes were not detected in 25 g samples. Generally, less than 102 cfu/g of Staphylococcus aureus, Escherichia coli, Pseudomonas spp., Enterobacteriaceae, and molds were present in the fermented foods. Bacillus cereus group members (<102 to 2.3 × 104 cfu/g), lactic acid bacteria (<102 to 1.1 × 107 cfu/g), halophilic and halotolerant bacteria (<102 to 8.9 × 106 cfu/g), sulfite-reducing Clostridium spp. (<102 to 3.5 × 106 cfu/g), and yeasts (<102 to 1.1 × 106 cfu/g) were detected in this study. Still, the presence of pathogenic and spoilage microorganisms in these fermented foods was within the acceptable ranges. Putrescine, cadaverine, tyramine, and histamine were detected in 100%, 89%, 81%, and 75% of the tested products, respectively. The concentrations of histamine (>500 ppm) and tyramine (>600 ppm) were higher than the recommended maximum levels in respectively four and one of 57 fermented foods, which represents a potential health risk. The results suggest that the production process, distribution, and domestic handling of fermented foods should be re-evaluated. Further research is needed for the establishment of applicable preservation techniques in Cambodia.

Short communication: Clostridial spore counts in vat milk of Alpine dairies

One of the most severe quality defects in hard and semi-hard cheese, the late blowing defect, is caused by endospore-forming bacteria of the genus Clostridium. To minimize financial losses and waste of resources due to cheese spoilage, raw milk with elevated clostridial spore counts should not be used for the production of certain cheese types. In this context, threshold values of clostridial spore concentrations that cause quality defects in cheese are still under debate. To improve our understanding about late blowing defects, further information on the correlation between clostridial spore concentrations in milk and cheese quality is indispensable. Thus, the aim of this study was to monitor the microbiological quality of milk used for Alpine cheese production regarding clostridial endospore levels to facilitate the establishment of threshold spore concentrations that guarantee the absence of quality defects in Austrian cheese. For this purpose, we monitored clostridial endospore levels in vat milk of 4 Alpine dairies throughout the summer grazing period in 2018. Surprisingly, we observed almost complete absence of butyric acid-producing clostridia in milk and no blowing defects in cheese. Hence, critical clostridial spore concentrations could not be verified. Moreover, the observed low spore levels reveal that the prohibition of silage feeding and good farming practices effectively minimize clostridial endospore counts in milk and ensure the manufacture of high-quality cheese even if technological possibilities are limited.

Lactic Acid Bacteria Isolation from Spontaneous Sourdough and Their Characterization Including Antimicrobial and Antifungal Properties Evaluation

This research effort aimed at isolating and phenotypically characterizing lactic acid bacteria (LAB) isolates from a spontaneous rye sourdough manufactured following traditional protocols, as well as at evaluating their antimicrobial and antifungal properties as key features for future industrial applications. Thirteen LAB strains of potential industrial interest were isolated and identified to species-level via PCR. Most of the sourdough isolates showed versatile carbohydrate metabolisms. The Leuconostoc mesenteroides No. 242 and Lactobacillus brevis No. 173 demonstrated to be gas producers; thus, revealing their heterofermenter or facultative homofermenter features. Viable counts higher than 7.0 log10 (CFU/mL) were observed for Lactobacillus paracasei No. 244, Lactobacillus casei No. 210, L. brevis No. 173, Lactobacillus farraginis No. 206, Pediococcus pentosaceus No. 183, Lactobacillus uvarum No. 245 and Lactobacillus plantarum No. 135 strains, after exposure at pH 2.5 for 2 h. Moreover, L. plantarum No. 122, L. casei No. 210, Lactobacillus curvatus No. 51, L. paracasei No. 244, and L. coryniformins No. 71 showed growth inhibition properties against all the tested fifteen pathogenic strains. Finally, all LAB isolates showed antifungal activities against Aspergillus nidulans, Penicillium funiculosum, and Fusarium poae. These results unveiled the exceptionality of spontaneous sourdough as a source of LAB with effective potential to be considered in the design of novel commercial microbial single/mixed starter cultures, intended for application in a wide range of agri-food industries, where the antimicrobial and antifungal properties are often sought and necessary. In addition, metabolites therefrom may also be considered as important functional and bioactive compounds with high potential to be employed in food and feed, as well as cosmetic and pharmaceutical applications.

The Influence of Meat Batter Composition and Sausage Diameter on Microbiota and Sensory Traits of Artisanal Wild Boar Meat Sausages

In this study, the influence of meat batter composition and sausage diameter on the development of microbiota and sensory traits of traditional, spontaneously fermented wild boar meat sausages are evaluated. This research also demonstrates how principal component analysis (PCA) can be used to relate product sensory properties to particular microbial genotype and to select potential starter or adjunct culture. Generally, similar microbiological results were obtained in all types of products. The undesirable microbiota was either not detected at any sausage production stage or its number decreased below the detection limit in ripened sausages. The low growth rate of lactic acid bacteria (LAB) was consistent with the obtained pH and slow acidification rate. Although no differences in the composition of LAB species were noticed between sausage types (50S=50% wild boar meat in small casing, 50L=50% wild boar meat in large casing, 100S=100% wild boar meat in small casing), a clear separation based on LAB genotypes could be observed. Upon quantitative descriptive analysis, significant differences in sensory attributes between sausage types were established. According to the PCA, the overall acceptability traits of sausages are closely linked to one Leuconostoc mesenteroides genotype (LM_4). Of all tested technological properties, LM_4 strains showed remarkable acidification ability, lowering the pH from pH=5.41 to 3.74, and pronounced proteolytic activity on skimmed milk as well as antagonistic activity against Staphylococcus aureus (DSM 20231) and Brochothrix thermosphacta (LMG 17208). Lipolytic and haemolytic activities were not detected, and all analyzed strains were susceptible to tested antibiotics and possessed no biogenic amine genes.

Identification, Classification and Screening for γ-Amino-butyric Acid Production in Lactic Acid Bacteria from Cambodian Fermented Foods

Screening for various types of lactic acid bacteria (LAB) that form the biological agent γ-amino-butyric acid (GABA) is important to produce different kinds of GABA-containing fermented foods. So far, no GABA-producing LAB have been reported from Cambodian fermented foods. Most small-scale fermentations and even some industrial processes in this country still rely on indigenous LAB. The application of GABA-producing autochthonous starters would allow the production of Cambodian fermented foods with an additional nutritional value that meet the population's dietary habits and that are also more attractive for the international food market. Matrix-assisted laser desorption/ionizing time-of-flight mass spectrometry (MALDI-TOF MS) and partial 16S rDNA sequencing were used to identify 68 LAB isolates from Cambodian fermented foods. These isolates were classified and grouped with (GTG)5 rep-PCR, resulting in 50 strains. Subsequently, all strains were investigated for their ability to produce GABA by thin layer chromatography. GABA-positive strains were further analyzed by the GABase assay. Of the six GABA-positive LAB strains-one Lactobacillus futsaii, two Lactobacillus namurensis, and three Lactobacillus plantarum strains-two Lactobacillus plantarum strains produced high amounts of GABA (20.34 mM, 16.47 mM). These strains should be further investigated for their potential application as GABA-producing starter cultures in the food applications.

Whole Genome Sequencing-Based Comparison of Food Isolates of Cronobacter sakazakii

Cronobacter sakazakii is an emerging foodborne pathogen, which is linked to life-threatening infections causing septicemia, meningitis, and necrotizing enterocolitis. These infections have been epidemiologically connected to ingestion of contaminated reconstituted powder infant formula. Even at low water activity C. sakazakii can survive for a long time; it is capable of protective biofilm formation and occasionally shows high virulence and pathogenicity even following stressful environmental conditions. Hence it is a challenging task for the food industry to control contamination of food ingredients and products through the entire production chain, since an increasing number of severe food-related outbreaks of C. sakazakii infections has been observed. The seemingly great capability of C. sakazakii to survive even strict countermeasures combined with its prevalence in many food ingredients requires a greater in depth understanding of its virulence factors to master the food safety issues related to this organism. In this context, we present the whole genome sequence (WGS) of two different C. sakazakii isolated from skimmed milk powder (C7) and ready-to-eat salad mix (C8), respectively. These are compared to other, already sequenced, C. sakazakii genomes. Sequencing of the fusA allele revealed that both isolates were C. sakazakii. We investigated the molecular characteristics of both isolates relevant for genes associated with pathogenesis and virulence factors, resistance to stressful environmental conditions (e.g., osmotic and heat), survival in desiccation as well as conducted a comparative genomic analysis. By using multi-locus sequence typing (MLST), the genetic type of both isolates is assessed and the number of unique genes is determined. DNA of C. sakazakii C8 is shown to hold a novel and unique sequence type; the number of unique genes identified in the genomic sequence of C. sakazakii C7 and C8 were 109 and 188, respectively. Some of the determined unique genes such as the rhs and VgrG genes are linked to the Type VI Secretion System cluster, which is associated with pathogenicity and virulence factors. Moreover, seven genes encoding for multi-drug resistance were found in both isolates. The finding of a number of genes linked to producing capsules and biofilm are likely related to the observed resistance to desiccation.

Prevalence of antibiotic-resistant E. coli in broilers challenged with a multi-resistant E. coli strain and received ampicillin, an organic acid-based feed additive or a synbiotic preparation

The aim of this study was to evaluate the effect of ampicillin, an organic acid-based feed additive and a synbiotic preparation on the prevalence of antibiotic-resistant E. coli in the ceca of broilers. A total of 2000 broiler chickens (Ross 708) were randomly assigned to 5 groups with 8 replicates. The negative control group was the only group that was not subjected to avian pathogenic E. coli challenge, while all the other 4 groups received a multi-resistant E. coli strain that was resistant to ampicillin, cephalexin, and nalidixic acid as an oral challenge. The second group served as a challenge control, and the third group received the antibiotic ampicillin via water for 5 d. The fourth group received a feed additive based on organic acids and cinnamaldehyde, and the fifth group received a synbiotic preparation via feed and water. On day 17 and 38 of the trial, cecal samples from 3 birds from each of the 40 pens were obtained, and the E. coli counts and abundances of antibiotic-resistant E. coli were determined. Oral challenge with an avian pathogenic E. coli strain did not influence the performance, and there was no significant difference in growth performance between groups. The total E. coli count was lower (P < 0.05) in the group supplemented with the synbiotic than in the challenge control group on day 38 of the trial. Administration of an antibiotic for 5 d led to a significant increase in the abundance of E. coli strains resistant to ampicillin, amoxicillin-clavulanic acid, cefoxitin, and ceftriaxone. There was no increase in the abundance of antibiotic-resistant E. coli observed in the groups that received feed supplemented with an organic acid/cinnamaldehyde-based feed additive or a synbiotic. Moreover, the effects of the tested feed additives on the prevalence of resistant E. coli are demonstrated by the lower ceftriaxone minimal inhibitory concentration values for this group than for the antibiotic group. Additionally, the synbiotic group exhibited lower ceftriaxone minimal inhibitory concentration values than the antibiotic group.

The application of antibiotics in broiler production and the resulting antibiotic resistance in Escherichia coli: A global overview

The increase in antibiotic resistance is a global concern for human and animal health. Resistant microorganisms can spread between food-producing animals and humans. The objective of this review was to identify the type and amount of antibiotics used in poultry production and the level of antibiotic resistance in Escherichia coli isolated from broilers. Isolate information was obtained from national monitoring programs and research studies conducted in large poultry-producing regions: US, China, Brazil, and countries of EU-Poland, United Kingdom, Germany, France, and Spain. The survey results clearly display the absence of a harmonized approach in the monitoring of antibiotics per animal species and the evaluation of resistances using the same methodology. There is no public long-term quantitative data available targeting the amount of antibiotics used in poultry, with the exception of France. Data on antibiotic-resistant E. coli are available for most regions but detection of resistance and number of isolates in each study differs among regions; therefore, statistical evaluation was not possible. Data from France indicate that the decreased use of tetracyclines leads to a reduction in the detected resistance rates. The fluoroquinolones, third-generation cephalosporins, macrolides, and polymyxins ("highest priority critically important" antibiotics for human medicine according to WHO) are approved for use in large poultry-producing regions, with the exception of fluoroquinolones in the US and cephalosporins in the EU. The approval of cephalosporins in China could not be evaluated. Tetracyclines, aminoglycosides, sulfonamides, and penicillins are registered for use in poultry in all evaluated countries. The average resistance rates in E. coli to representatives of these antibiotic classes are higher than 40% in all countries, with the exception of ampicillin in the US. The resistance rates to fluoroquinolones and quinolones in the US, where fluoroquinolones are not registered for use, are below 5%, while the average of resistant E. coli is above 40% in Brazil, China, and EU, where use of fluoroquinolones is legalized. However, banning of fluoroquinolones and quinolones has not totally eliminated the occurrence of resistant populations.

Characterization of Biofilm Formation by Cronobacter spp. Isolates of Different Food Origin under Model Conditions

Cronobacter spp. are opportunistic human pathogens that cause serious diseases in neonates and immunocompromised people. Owing to their biofilm formation on various surfaces, both their detection and their removal from production plants constitute a major challenge. In this study, food samples were randomly collected in Austria and examined for the presence of Cronobacter spp. Presumptive isolates were identified by a polyphasic approach. Five percent of the samples were positive for C. sakazakii and 2.4% for C. dublinensis. Individual growth of the isolates was characterized based on lag time, growth rate, and generation time. During an incubation period of 6 to 72 h, biofilm formation of 11 selected isolates was quantified under model conditions by a crystal violet staining assay with 96-well plates with different carbon sources (lactose, glucose, maltose, sucrose, and sodium acetate) and NaCl levels and under variable temperature and pH conditions. Biofilm formation was more pronounced at lactose concentrations between 0.25 and 3% compared with 5% lactose, which lead to thinner layers. C. sakazakii isolate C7, isolated from infant milk powder, was the strongest biofilm producer at 10 mM Mg²⁺ and 5 mM Mn²⁺, 0.5% sodium acetate, at pH levels between 7 and 9 at 37°C for 24 h. C. sakazakii strain C6 isolated from a plant air filter was identified as a moderate biofilm former and C. sakazakii strain DSM 4485, a clinical isolate, as a weak biofilm former. Based on PCR detection, genes bcsA, bcsB, and bcsG encoding for cellulose could be identified as markers for biofilm formation. Isolates carrying bcsA and bcsB showed significantly stronger biofilm formation than isolates without these genes ( P < 0.05), in strong correlation with the results obtained in the crystal violet assay. Further investigations using confocal laser scanning microscopy revealed that extracellular polymeric substances and glycocalyx secretions were the dominating components of the biofilms and that the viable fraction of bacteria in the biofilm decreased over time.

Fermentability of a Novel Galacto-Oligosaccharide Mixture by Lactobacillus spp. and Bifidobacterium spp

This study aimed to investigate the specific growth stimulation of certain desired intestinal bacteria by a novel galacto-oligosaccharide mixture, which was produced with a β-galactosidase from a potential probiotic Lactobacillus isolate that contained mainly oligosaccharides of β-1,3 and β-1,6 glycosidic linkages (termed Lb-GOS) using single-strain fermentations. The composition of this Lb-GOS mixture was 33.5% disaccharides, 60.5% trisaccharides, 4.8% tetrasaccharides, and 1.0% pentasaccharides with a negligible amount of monosaccharides, lactose, and lactobionic acid (0.3%). Eight Lactobacillus spp. strains and three Bifidobacterium spp. strains were used in single-strain fermentations to determine the fermentation activity scores of this Lb-GOS preparation compared to two commercially available prebiotic mixtures, 4′GOS-P and Vivinal GOS (V-GOS). The highest scores were obtained when L. reuteri Lb46 and the two Bifidobacterium strains, B. animalis subsp. lactis Bif1 and Bif3, were grown on these galacto-oligosaccharide mixtures. In addition, the Lb-GOS mixture was found to have higher fermentation activity scores; hence, it stimulated the growth of these probiotic strains more than 4′GOS-P and V-GOS, which may be attributed to the different glycosidic linkage types that are found in the Lb-GOS mixture compared to the other two commercial preparations. These findings suggested that the Lb-GOS mixture that is described in this work should be of interest for the formulations of new carbohydrate-based functional food ingredients.

Assessment of Microbial Community Dynamics in River Bank Filtrate Using High-Throughput Sequencing and Flow Cytometry

Surface-groundwater interactions play an important role in microbial community compositions of river bank filtrates. Surface water contaminations deriving from environmental influences are attenuated by biogeochemical processes in the hyporheic zone, which are essential for providing clean and high-quality drinking water in abstraction wells. Characterizing the flow regime of surface water into the groundwater body can provide substantial information on water quality, but complex hydraulic dynamics make predictions difficult. Thus, a bottom up approach using microbial community shifting patterns as an overall outcome of dynamic water characteristics could provide more detailed information on the influences that affect groundwater quality. The combination of high-throughput sequencing data together with flow cytometric measurements of total cell counts reveals absolute abundances among taxa, thus enhancing interpretation of bacterial dynamics. 16S rRNA high-throughput sequencing of 55 samples among six wells in a well field in Austria that is influenced by river bank filtrate within a time period of 3 months has revealed both, clear differences as well as strong similarity in microbiome compositions between wells and dates. A significant community shift from April to May occurred in four of six wells, suggesting that surface water flow regimes do affect these wells stronger than others. Triplicate sampling and subsequent sequencing of wells at different dates proved the method to be reproducible. Flow cytometric measurements of total cells indicate microbial shifts due to increased cell counts and emphasize the rise of allochthonous microorganisms. Typical freshwater bacterial lineages (Verrucomicrobia, Bacteroidetes, Actinobacteria, Cyanobacteria, Armatimonadetes) were identified as most increasing phyla during community shifts. The changes are most likely a result of increased water abstraction in the wells together with constant river water levels rather than rain events. The results provide important knowledge for future implementations of well utilization in dependency of the nearby Danube River water levels and can help drawing conclusions about the influence of surface water in the groundwater such that hygienically save and clean drinking water with a stable microbial community can be provided.

Applicability of Yeast Fermentation to Reduce Fructans and Other FODMAPs

A diet low in fermentable oligosaccharides, disaccharides, monosaccharides and, polyols (FODMAPs) is recommended for people affected by irritable bowel syndrome (IBS) and non-coeliac wheat sensitivity (NCWS) in order to reduce symptoms. Therefore, the aim of this study was to evaluate the impact of 13 sourdough-related yeasts on FODMAP degradation, especially fructans. First, a model system containing a typical wheat carbohydrate profile was applied to evaluate the growth rate of each yeast strain. Additionally, changes in the sugar composition, for up to four days, were monitored by high-pressure anion-exchange chromatography (HPAEC). A more realistic approach with a wheat flour suspension was used to characterize CO₂ production according to the Einhorn method. The reduction of the total fructans was analyzed using an enzymatic method. Furthermore, a fingerprint of the present fructans with different degrees of polymerization was analyzed by HPAEC. The results revealed strong differences in the examined yeast strains' ability to degrade fructans, in both the model system and wheat flour. Overall, Saccharomycescerevisiae isolated from Austrian traditional sourdough showed the highest degree of degradation of the total fructan content and the highest gas building capacity, followed by Torulasporadelbrueckii. Hence, this study provides novel knowledge about the FODMAP conversion of yeast strains.

Effect of an organic acids based feed additive and enrofloxacin on the prevalence of antibiotic-resistant E. coli in cecum of broilers

Increasing antibiotic resistance is a major public health concern. Fluoroquinolones are used to treat and prevent poultry diseases worldwide. Fluoroquinolone resistance rates are high in their countries of use. The aim of this study was to evaluate the effect of an acids-based feed additive, as well as fluoroquinolone antibiotics, on the prevalence of antibiotic-resistant E. coli. A total of 480 broiler chickens (Ross 308) were randomly assigned to 3 treatments: a control group receiving a basal diet; a group receiving a feed additive (FA) based on formic acid, acetic acid and propionic acid; and an antibiotic enrofloxacin (AB) group given the same diet, but supplemented with enrofloxacin in water. A pooled fecal sample of one-day-old chicks was collected upon arrival at the experimental farm. On d 17 and d 38 of the trial, cecal samples from each of the 8 pens were taken, and the count of E. coli and antibiotic-resistant E. coli was determined.The results of the present study show a high prevalence of antibiotic-resistant E. coli in one-day-old chicks. Supplementation of the diet with FA and treatment of broilers with AB did not have a significant influence on the total number of E. coli in the cecal content on d 17 and d 38 of the trial. Supplementation with FA contributed to better growth performance and to a significant decrease (P ≤ 0.05) in E. coli resistant to ampicillin and tetracycline compared to the control and AB groups, as well as to a decrease (P ≤ 0.05) in sulfamethoxazole and ciprofloxacin-resistant E. coli compared to the AB group. Treatment with AB increased (P ≤ 0.05) the average daily weight compared to the control group and increased (P ≤ 0.05) the number of E. coli resistant to ciprofloxacin, streptomycin, sulfamethoxazole and tetracycline; it also decreased (P ≤ 0.05) the number of E. coli resistant to cefotaxime and extended spectrum beta-lactamase- (ESBL-) producing E. coli in the ceca of broilers.

Effects of selected lactobacilli on the functional properties and stability of gluten-free sourdough bread

The aim of this investigation was to determine the influence of seven different Lactobacillus spp. (Lb.) strains compared with a commercial starter culture (CS) on the functional properties of gluten-free (GF) sourdough-breads. The sourdough stability of selected strains was also evaluated upon back-slopping. Results showed that the bread properties were greatly affected by the Lb. strains. Millet breads achieved lower specific volumes (1.80–2.19 cm³/g), higher crumb firmness (19.01–42.19 N) and lower relative elasticities (21.5–43.4%) than buckwheat breads. Compared with the CS, Lactobacillus pentosus and Lb. hammesii positively influenced the crumb firmness of buckwheat and millet breads, respectively, while Lb. paralimentarius enhanced this property in both breads. Only one of the two Lactobacillus sanfranciscencis strains was able to improve all functional properties in both GF breads. Back-slopping of the sourdoughs revealed stable properties in case of buckwheat, while maturity of the millet sourdough could not be reached. These observations were supported by the microbial count, metabolite production and carbohydrate consumption. Mature sourdough significantly improved the crumb firmness and porosity of the GF breads. These results highlighted the importance of selecting the appropriate lactic acid bacteria strains, to maximize the quality of GF bread.

Influence of Orally Administered Probiotic Lactobacillus Strains on Vaginal Microbiota in Women with Breast Cancer during Chemotherapy: A Randomized Placebo-Controlled Double-Blinded Pilot Study

Background

Due to chemotherapy and estrogen deprivation therapy, genitourinary syndrome of menopause is a common condition in breast cancer patients. We aimed to determine the effect of an orally administered Lactobacillus preparation on the vaginal microbiota in breast cancer patients.

Methods

Postmenopausal breast cancer patients receiving chemotherapy, with vaginal atrophy and an intermediate vaginal microbiota (Nugent score 4-6), were either randomized to the intervention group receiving probiotic capsules of 4 Lactobacillus species or to the control group receiving placebo twice daily for 2 weeks. Consecutive vaginal swabs were taken at baseline, 1 day after administration of the last capsule (follow-up 1), and after 1 week (follow-up 2) in 22 patients (11 vs. 11).

Results

We observed a positive influence on the vaginal microbiota in 7/11 (63%) women in the intervention group, and 4/11 (36%) women in the control group. There was a shift in Nugent score towards normal microbiota levels in the intervention group (-1.3 at follow-up 1, -0.45 at follow-up 2) and a significant deterioration of the Nugent score in the control group (+0.4 at follow-up 1, +2.5 at follow-up 2).

Conclusion

The orally administered Lactobacillus preparation has the potential to improve the vaginal microbiota in women undergoing chemotherapy for breast cancer.

Effect of a yoghurt drink containing Lactobacillus strains on bacterial vaginosis in women - a double-blind, randomised, controlled clinical pilot trial

Bacterial vaginosis (BV) is characterised by a depletion of lactobacilli in favour of an overgrowth of anaerobic bacteria. It is associated with increased risk for urogenital infections and abortion. In this study we assessed the effect of a yoghurt drink containing Lactobacillus strains on BV. The strains had been isolated from healthy pregnant women and selected for acidification capacity, production of H₂O₂, glycogen utilisation, bile salt tolerance and inhibition of pathogens. Using Amsel criteria BV was diagnosed in 36 women aged ≥18 years with stable menstrual cycle or menopause. They were treated with oral metronidazole for 7 days (2×500 mg/d). Starting with the treatment, women consumed twice daily either verum or placebo during 4 weeks. Verum was 125 g yoghurt containing (besides Lactobacillus delbrueckii ssp. bulgaricus and Streptococcus thermophilus) living strains Lactobacillus crispatus LbV 88 (DSM 22566), Lactobacillus gasseri LbV 150N (DSM 22583), Lactobacillus jensenii LbV 116 (DSM 22567) and Lactobacillus rhamnosus LbV96 (DSM 22560), each 1×107 cfu/ml; placebo was 125 g chemically acidified milk. After 4 weeks of intervention 0 of 17 had BV in the verum group versus 6 of 17 in the s.a. control (0.018 in Fisher Exact test). Amsel score decreased during the intervention period by 4.0 (median) (4.0; 3.0) (25^th; 75^th percentile) in the verum group compared to 2.0 (4.0; 0.0) in the control group (P=0.038 in Mann-Whitney test). Discharge and odour (Amsel criteria 2+3) also decreased by 2.0 (2.0; 1.0) in the verum compared to 1.0 (2.0; 0.0) in the control group (P=0.01) and differed after 4 weeks intervention between the groups 0.0 (0.0; 0.0) versus 1.0 (0.0; 2.0) (P=0.001). Nugent score decreased during the intervention period by 5.5 (7.0;2.3) in the verum compared to 3.0 (6.0;0.5) in the control group (P=0.158). Additional intake of yoghurt containing these probiotic strains improved the recovery rate and symptoms of BV and tended to improve the vaginal microbial pattern.

The effect of negative pressure wound therapy with antibacterial dressings or antiseptics on an in vitro wound model

OBJECTIVE

The aim of this study was to investigate the bacterial bioburden in experimental in vitro wounds during the application of conventional negative pressure wound therapy (NPWT), with and without antimicrobial dressings (polyhexanide, silver), against NPWT instillation of octenidine.

METHOD

Experimental wounds produced in an in vitro porcine wound model were homogenously contaminated with bacterial suspension and treated with NPWT and different options. Group A: non-antimicrobial polyurethane foam dressing; group B: antimicrobial polyurethane foam dressing containing silver; group C: antimicrobial gauze dressing containing polyhexanide; group D: non-antimicrobial polyurethane foam dressing intermittently irrigated with octenidine; group E: negative control (non-antimicrobial polyurethane foam dressing without NPWT). Standard biopsies were harvested after 24 and 28 hours.

RESULTS

This study demonstrated that the use of NPWT with intermitted instillation of octenidine (group D) or application of silver-based polyurethane foam dressings (group B) is significantly superior against Staphylococcus aureus colonisation in experimental wounds compared with non-antimicrobial polyurethane foam dressing (group A) after 48 hours. Surprisingly, the polyhexanide-based dressing (group C) used in this model showed no statistical significant effect compared with the control group (group E) after 24 or 48 hours of treatment.

CONCLUSION

Both intermitted instillation of octenidine and silver-based dressings in standard NPWT were significantly superior compared with non-antimicrobial polyurethane foam dressings or PHMB coated gauze dressing after 48 hours.

Lactococci of Local Origin as Potential Starter Cultures for Traditional Montenegrin Cheese Production

The aim of this study is to characterise and examine the biochemical properties of 40 Lactococcus lactis strains isolated from indigenous Montenegrin dairy products in order to explore their potential to be used as starter cultures for producing typical Montenegrin cheese, such as 'bijeli sir', 'masni sir' and 'njeguški sir'. Their safety regarding the production of biogenic amines, the presence of antimicrobial resistance and the antibacterial activity against relevant pathogens and spoilage microorganisms has also been tested. Based on the characterisation, all strains belong to L. lactis ssp. lactis. Out of these 40 strains, 23 displayed rapid acidification ability and proteolysis. However, none of the strains exhibited the ability of lipid degradation. Most of the strains were not associated with any health risk investigated. Summing up, a large percentage (27.5%) of the tested strains showed good properties. These strains should be further examined for their possible application as specific starter cultures in the production of indigenous cheese in Montenegro.

The intestinal microbiota of piglets fed with wheat bran variants as characterised by 16S rRNA next-generation amplicon sequencing

The intestinal microbiota of piglets fed with a Control diet low in dietary fibre and modified wheat bran variants as an additional source of insoluble dietary fibre was characterised. In this context, variances in the microbiota of three different gut segments were assessed. Wheat bran was either included in its native form or modified by fermentation and extrusion before added at 150 g/kg to a basal diet for 48 piglets (12 animals per treatment). Total DNA was extracted from digesta samples from the jejunum, the end of the ileum and the colon ascendens. Samples were prepared accordingly for subsequent sequencing with the Illumina MiSeq. The obtained results revealed distinct location-specific differences in microbial composition. While Firmicutes were most predominant in all three gut segments, Bacteroidetes were additionally found in the colon at high abundance. The parameters of alpha and beta diversity analysis showed significant differences (p < 0.01) between the colon and the other two gut segments. Specialised bacterial groups like Prevotella and Ruminococcaceae were among the most predominant ones found in the colon, as they possess cellulolytic properties to degrade (at least partially) non-starch polysaccharides, while their abundance was negligible in the jejunum and the ileum. Conversely, the genera Lactobacillus, Bifidobacterium and Veillonella, for example, were among the most predominant groups in the jejunum and ileum, while in the colon they were hardly found. Although statistical taxonomical evaluation, following p-value correction, did not reveal pronounced differences in abundance related to bran modification, alpha and beta diversity analysis showed an influence regarding the various feeding strategies applied. Based on these findings, a more in-depth view on intestinal microbial composition within the gastrointestinal tract of young pigs fed with low- and high-fibre diets was generated.

Tetracycline Resistance Patterns of Lactobacillus buchneri Group Strains

Lactobacilli are applied as starter cultures for controlled fermentation in the production of food and feed. Among other lactobacilli, members of the Lactobacillus buchneri group are used in fermented milk, wine, and silage. Most of the L. buchneri species used for the manufacturing of food or feed are already on the list for qualified presumption of safety status and are recommended as biological agents by the European Food Safety Authority. Consequently, new strains intended as food or feed additives do not require any additional safety check than confirming the absence of transferable antibiotic resistance determinants. Of these determinants, tetracycline resistance genes are especially predominant in lactobacilli. Within this study, a total of 128 strains belonging to the L. buchneri group ( L. buchneri , L. diolivorans , L. farraginis , L. hilgardii , L. kefiri , L. kisonensis , L. otakiensis , L. parabuchneri , L. parafarraginis , L. parakefiri , L. rapi , L. senioris , and L. sunkii ) were examined for their susceptibility to tetracycline. Tetracycline MICs were assessed by the broth microdilution method according to ISO 10932/IDF 223. Subsequently, the presence of tetracycline resistance genes was investigated by using PCR. In addition, selected strains were tested for a broader range of tetracycline resistance genes by using a microarray technique. Applying the tetracycline cutoff values defined by European Food Safety Authority for heterofermentative and obligately homofermentative lactobacilli, 96.9% of the strains would have been categorized as tetracycline resistant. However, none of the tested tetracycline resistance genes could be detected by PCR or microarray analysis. Furthermore, the MIC distribution of all strains was unimodal and at the high end of the tested tetracycline concentration range (4 to 256 μg/ml). Thus, these data suggest that tetracycline resistance in the L. buchneri group strains is intrinsic, which complies with the requirements defined in the qualified presumption of safety outline.

Comparison of the CLSI guideline and ISO/IDF standard for antimicrobial susceptibility testing of Lactobacilli

Lactobacilli play a crucial role as probiotics and as starter cultures in the production of fermented foods. Although lactobacilli are a technologically useful and beneficial group of bacteria, a few members of them have been rarely correlated with bacterial infections. Correspondingly, clinicians are interested in the antimicrobial susceptibility of lactobacilli. In addition, antimicrobial susceptibility testing (AST) is also relevant for commercially applied lactobacilli as bacterial strains harboring transferable antibiotic resistance genes should not be used in fermented and probiotic foods. Therefore, two methods were developed by different organizations, which were compared within this study. For this purpose, 22 Lactobacillus-type strains were tested for their antimicrobial susceptibility to 16 antibiotics following the procedures of the Clinical and Laboratory Standards Institute (CLSI) and the International Organization of Standardization (ISO)/International Dairy Federation (IDF). Crucial discrepancies between both procedures were detected mainly due to the different AST media. Hence, half of the strains tested did not consistently grow in the CLSI medium, whereas all showed evaluable growth in the ISO/IDF medium. However, some antibiotics were influenced by the latter medium. In particular, low levels of essential agreement between both methods were obtained with seven antibiotics. Accordingly, different interpretative criteria are needed for both procedures to distinguish resistant from susceptible strains.

Phylogenetic diversity and biological activity of culturable Actinobacteria isolated from freshwater fish gut microbiota

The diversity of Actinobacteria isolated from the gut microbiota of two freshwater fish species namely Schizothorax zarudnyi and Schizocypris altidorsalis was investigated employing classical cultivation techniques, repetitive sequence-based PCR (rep-PCR), partial and full 16S rDNA sequencing followed by phylogenetic analysis. A total of 277 isolates were cultured by applying three different agar media. Based on rep-PCR profile analysis a subset of 33 strains was selected for further phylogenetic investigations, antimicrobial activity testing and diversity analysis of secondary-metabolite biosynthetic genes. The identification based on 16S rRNA gene sequencing revealed that the isolates belong to eight genera distributed among six families. At the family level, 72% of the 277 isolates belong to the family Streptomycetaceae. Among the non-streptomycetes group, the most dominant group could be allocated to the family of Pseudonocardiaceae followed by the members of Micromonosporaceae. Phylogenetic analysis clearly showed that many of the isolates in the genera Streptomyces, Saccharomonospora, Micromonospora, Nocardiopsis, Arthrobacter, Kocuria, Microbacterium and Agromyces formed a single and distinct cluster with the type strains. Notably, there is no report so far about the occurrence of these Actinobacteria in the microbiota of freshwater fish. Of the 33 isolates, all the strains exhibited antibacterial activity against a set of tested human and fish pathogenic bacteria. Then, to study their associated potential capacity to synthesize diverse bioactive natural products, diversity of genes associated with secondary-metabolite biosynthesis including PKS I, PKS II, NRPS, the enzyme PhzE of the phenazine pathways, the enzyme dTGD of 6-deoxyhexoses glycosylation pathway, the enzyme Halo of halogenation pathway and the enzyme CYP in polyene polyketide biosynthesis were investigated among the isolates. All the strains possess at least two types of the investigated biosynthetic genes, one-fourth of them harbours more than four. This study demonstrates the significant diversity of Actinobacteria in the fish gut microbiota and it's potential to produce biologically active compounds.

Rectal Lactobacillus species and their influence on the vaginal microflora: a model of male-to-female transsexual women

INTRODUCTION

Based on Lactobacillus species co-colonizing the vagina and rectum, it has been hypothesized that the rectum may be an important reservoir for vaginal colonization by lactobacilli. There are no data on this issue in male-to-female transsexual women.

AIM

We undertook this observational study to characterize the Lactobacillus species present in the neovagina and rectum of male-to-female transsexual women and to determine the degree of neovaginal-rectal co-colonization in order to gain a better understanding of the potential role of the gut as a reservoir for genital lactobacilli.

METHODS

Sixty-one male-to-female transsexual women with penile skin lined neovagina without clinical signs of infection were recruited on an ongoing basis from among male-to-female transsexual outpatients. Neovaginal and rectal smears were taken for molecular Lactobacillus species profiling by denaturing gradient gel electrophoresis (PCR-DGGE).

MAIN OUTCOME MEASURES

Matching Lactobacillus species between neovagina and rectum.

RESULTS

Forty-three of the 61 male-to-female transsexual women (70.5%) simultaneously harbored the same lactobacilli in both the neovagina and rectum. We found 276 neovaginal and 258 rectal DGGE bands representing 11 Lactobacillus species, with 201 matches of the same Lactobacillus species in neovagina and rectum. 37 of the 61 women (61%) had two or more matching Lactobacillus species.

CONCLUSION

These data support the hypothesis that the rectum may play an important role as source of Lactobacillus species that colonies neovagina of male-to-female transsexual women. In view of the specific anatomical circumstances of the study population, these findings may be extended to the general population of women.