Dietary Live Yeast Supplementation Influence on Cow’s Milk, Teat and Bedding Microbiota in a Grass-Diet Dairy System

The supplementation of animal feed with microbial additives remains questioning for the traditional or quality label raw milk cheeses with regard to microbial transfer to milk. We evaluated the effect of dietary administration of live yeast on performance and microbiota of raw milk, teat skin, and bedding material of dairy cows. Two balanced groups of cows (21 primiparous 114 ± 24 DIM, 18 multiparous 115 ± 33 DIM) received either a concentrate supplemented with Saccharomyces cerevisiae CNCM I-1077 (1 × 1010 CFU/d) during four months (LY group) or no live yeast (C group). The microbiota in individual milk samples, teat skins, and bedding material were analysed using culture dependent techniques and high-throughput amplicon sequencing. The live yeast supplementation showed a numerical increase on body weight over the experiment and there was a tendency for higher milk yield for LY group. A sequence with 100% identity to that of the live yeast was sporadically found in fungal amplicon datasets of teat skin and bedding material but never detected in milk samples. The bedding material and teat skin from LY group presented a higher abundance of Pichia kudriavzevii reaching 53% (p < 0.05) and 10% (p < 0.05) respectively. A significant proportion of bacterial and fungal ASVs shared between the teat skin and the milk of the corresponding individual was highlighted.

Integration of Multiomic Data to Characterize the Influence of Milk Fat Composition on Cantal-Type Cheese Microbiota

A previous study identified differences in rind aspects between Cantal-type cheeses manufactured from the same skimmed milk, supplemented with cream derived either from pasture-raised cows (P) or from cows fed with maize silage (M). Using an integrated analysis of multiomic data, the present study aimed at investigating potential correlations between cream origin and metagenomic, lipidomic and volatolomic profiles of these Cantal cheeses. Fungal and bacterial communities of cheese cores and rinds were characterized using DNA metabarcoding at different ripening times. Lipidome and volatolome were obtained from the previous study at the end of ripening. Rind microbial communities, especially fungal communities, were influenced by cream origin. Among bacteria, Brachybacterium were more abundant in P-derived cheeses than in M-derived cheeses after 90 and 150 days of ripening. Sporendonema casei, a yeast added as a ripening starter during Cantal manufacture, which contributes to rind typical aspect, had a lower relative abundance in P-derived cheeses after 150 days of ripening. Relative abundance of this fungus was highly negatively correlated with concentrations of C18 polyunsaturated fatty acids and to concentrations of particular volatile organic compounds, including 1-pentanol and 3-methyl-2-pentanol. Overall, these results evidenced original interactions between milk fat composition and the development of fungal communities in cheeses.

Identification of Loci Enabling Stable and High-Level Heterologous Gene Expression

Efficient and reliable genome engineering technologies have yet to be developed for diatoms. The delivery of DNA in diatoms results in the random integration of multiple copies, quite often leading to heterogeneous gene activity, as well as host instability. Transgenic diatoms are generally selected on the basis of transgene expression or high enzyme activity, without consideration of the copy number or the integration locus. Here, we propose an integrated pipeline for the diatom, Phaeodactylum tricornutum, that accurately quantifies transgene activity using a β-glucuronidase assay and the number of transgene copies integrated into the genome through Droplet Digital PCR (ddPCR). An exhaustive and systematic analysis performed on 93 strains indicated that 42% of them exhibited high β-glucuronidase activity. Though most were attributed to high transgene copy numbers, we succeeded in isolating single-copy clones, as well as sequencing the integration loci. In addition to demonstrating the impact of the genomic integration site on gene activity, this study identifies integration sites for stable transgene expression in Phaeodactylum tricornutum.

Lactic Starter Dose Shapes S. aureus and STEC O26:H11 Growth, and Bacterial Community Patterns in Raw Milk Uncooked Pressed Cheeses

Adding massive amounts of lactic starters to raw milk to manage the sanitary risk in the cheese-making process could be detrimental to microbial diversity. Adjusting the amount of the lactic starter used could be a key to manage these adverse impacts. In uncooked pressed cheeses, we investigated the impacts of varying the doses of a lactic starter (the recommended one, 1×, a 0.1× lower and a 2× higher) on acidification, growth of Staphylococcus aureus SA15 and Shiga-toxin-producing Escherichia coli (STEC) O26:H11 F43368, as well as on the bacterial community patterns. We observed a delayed acidification and an increase in the levels of pathogens with the 0.1× dose. This dose was associated with increased richness and evenness of cheese bacterial community and higher relative abundance of potential opportunistic bacteria or desirable species involved in cheese production. No effect of the increased lactic starter dose was observed. Given that sanitary criteria were paramount to our study, the increase in the pathogen levels observed at the 0.1× dose justified proscribing such a reduction in the tested cheese-making process. Despite this, the effects of adjusting the lactic starter dose on the balance of microbial populations of potential interest for cheese production deserve an in-depth evaluation.

rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis

Bioinformatic tools for marker gene sequencing data analysis are continuously and rapidly evolving, thus integrating most recent techniques and tools is challenging. We present an R package for data analysis of 16S and ITS amplicons based sequencing. This workflow is based on several R functions and performs automatic treatments from fastq sequence files to diversity and differential analysis with statistical validation. The main purpose of this package is to automate bioinformatic analysis, ensure reproducibility between projects, and to be flexible enough to quickly integrate new bioinformatic tools or statistical methods. rANOMALY is an easy to install and customizable R package, that uses amplicon sequence variants (ASV) level for microbial community characterization. It integrates all assets of the latest bioinformatics methods, such as better sequence tracking, decontamination from control samples, use of multiple reference databases for taxonomic annotation, all main ecological analysis for which we propose advanced statistical tests, and a cross-validated differential analysis by four different methods. Our package produces ready to publish figures, and all of its outputs are made to be integrated in Rmarkdown code to produce automated reports.

DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products

Background

Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size of read sequences and differently curated classification databases. The close phylogenetic relationship between species encountered in dairy products, however, makes it crucial to annotate species accurately to achieve sufficient phylogenetic resolution for further downstream ecological studies or for food diagnostics. Curated databases dedicated to the environment of interest are expected to improve the accuracy and resolution of taxonomy annotation.

Results

We provide a manually curated database composed of 10’290 full-length 16S rRNA gene sequences from prokaryotes tailored for dairy products analysis (https://github.com/marcomeola/DAIRYdb).

The performance of the DAIRYdb was compared with the universal databases Silva, LTP, RDP and Greengenes. The DAIRYdb significantly outperformed all other databases independently of the classification algorithm by enabling higher accurate taxonomy annotation down to the species rank. The DAIRYdb accurately annotates over 90% of the sequences of either single or paired hypervariable regions automatically.

The manually curated DAIRYdb strongly improves taxonomic annotation accuracy for microbiome studies in dairy environments. The DAIRYdb is a practical solution that enables automatization of this key step, thus facilitating the routine application of NGS microbiome analyses for microbial ecology studies and diagnostics in dairy products.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5914-8) contains supplementary material, which is available to authorized users.

Dialogue between Staphylococcus aureus SA15 and Lactococcus garvieae strains experiencing oxidative stress

Background

Staphylococcus aureus is an important foodborne pathogen. Lactococcus garvieae is a lactic acid bacterium found in dairy products; some of its strains are able to inhibit S. aureus growth by producing H₂O₂. Three strains of L. garvieae from different origins were tested for their ability to inhibit S. aureus SA15 growth. Two conditions were tested, one in which H₂O₂ was produced (high aeration) and another one in which it was not detected (low aeration). Several S. aureus genes related to stress, H₂O₂-response and virulence were examined in order to compare their level of expression depending on the inoculated L. garvieae strain. Simultaneous L. garvieae H₂O₂ metabolism gene expression was followed.

Results

The results showed that under high aeration condition, L. garvieae strains producing H₂O₂ (N201 and CL-1183) inhibited S. aureus SA15 growth and impaired its ability to deal with hydrogen peroxide by repressing H₂O₂-degrading genes. L. garvieae strains induced overexpression of S. aureus stress-response genes while cell division genes and virulence genes were repressed. A catalase treatment partially or completely restored the SA15 growth. In addition, the H₂O₂ non-producing L. garvieae strain (Lg2) did not cause any growth inhibition. The SA15 stress-response genes were down-regulated and cell division genes expression was not affected. Under low aeration condition, while none of the strains tested exhibited H₂O₂-production, the 3 L. garvieae strains inhibited S. aureus SA15 growth, but to a lesser extent than under high aeration condition.

Conclusion

Taken together, these results suggest a L. garvieae strain-specific anti-staphylococcal mechanism and an H₂O₂ involvement in at least two of the tested L. garvieae strains.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1340-3) contains supplementary material, which is available to authorized users.

Fluorescence spectroscopy coupled with independent components analysis to monitor molecular changes during heating and cooling of Cantal-type cheeses with different NaCl and KCl contents

BACKGROUND

Reduction of NaCl content of cheeses has received considerable attention by research during the past decades because of its health effects. Nonetheless, NaCl reduction is a challenge since it plays an important role in cheese quality, such as structure, texture and functional properties. Several methods were used to evaluate the effect of NaCl on these attributes. In this study, Cantal-type cheeses with different salts (NaCl and KCl) were analyzed for their structure at a molecular level and rheological properties during heating (20-60 °C) and cooling (60-20 °C). The structure was investigated by synchronous fluorescence spectroscopy (SFS) and the rheological properties by small-amplitude oscillatory test.

RESULTS

Independent components analysis (ICA) gave three independent components that were attributed to coenzyme/Maillard reaction products (IC1), tryptophan (IC2) and vitamin A (IC3). Signal proportions of each IC depicted information regarding the changes in those fluorophores with salts, heating and cooling. In addition, canonical correlation analysis (CCA) of the IC proportions and rheological measurements related modifications at a molecular level evaluated by fluorescence to cheese texture (0.34 < R² < 0.99).

CONCLUSION

This study demonstrated that SFS can monitor and characterize modification of Cantal-type cheeses at a molecular level, based on the analysis of the fluorescence spectra by ICA. The nature of correlation between signal proportions and the rheological parameters depicted that rheological attributes of cheeses observed at the macroscopic level can be derived from fluorescence spectra. © 2017 Society of Chemical Industry.

Bacterial community assembly from cow teat skin to ripened cheeses is influenced by grazing systems

The objectives of this study were to explore bacterial community assembly from cow teat skin to raw milk cheeses and to evaluate the role of farming systems on this assembly using 16S rRNA gene high-throughput sequencing. The two grazing systems studied (extensive vs. semi-extensive) had a greater effect on the microbiota of cow teat skin than on that of raw milks and cheeses. On teat skin, the relative abundance of several taxa at different taxonomic levels (Coriobacteriia, Bifidobacteriales, Corynebacteriales, Lachnospiraceae, Atopobium, and Clostridium) varied depending on the grazing system and the period (early or late summer). In cheese, the abundance of sub-dominant lactic acid bacteria (LAB) varied depending on the grazing system. Overall, 85% of OTUs detected in raw milks and 27% of OTUs detected in ripened cheeses were also found on cow teat skin. Several shared OTUs were assigned to taxa known to be involved in the development of cheese sensory characteristics, such as Micrococcales, Staphylococcaceae, and LAB. Our results highlight the key role of cow teat skin as a reservoir of microbial diversity for raw milk, and for the first time, that cow teat skin serves as a potential source of microorganisms found in raw-milk cheeses.

New Insights into the Anti-pathogenic Potential of Lactococcus garvieae against Staphylococcus aureus Based on RNA Sequencing Profiling

The bio-preservation potential of Lactococcus garvieae lies in its capacity to inhibit the growth of staphylococci, especially Staphylococcus aureus, in dairy products and in vitro. In vitro, inhibition is modulated by the level of aeration, owing to hydrogen peroxide (H₂O₂) production by L. garvieae under aeration. The S. aureus response to this inhibition has already been studied. However, the molecular mechanisms of L. garvieae underlying the antagonism against S. aureus have never been explored. This study provides evidence of the presence of another extracellular inhibition effector in vitro. This effector was neither a protein, nor a lipid, nor a polysaccharide, nor related to an L-threonine deficiency. To better understand the H₂O₂-related inhibition mechanism at the transcriptome level and to identify other mechanisms potentially involved, we used RNA sequencing to determine the transcriptome response of L. garvieae to different aeration levels and to the presence or absence of S. aureus. The L. garvieae transcriptome differed radically between different aeration levels mainly in biological processes related to fundamental functions and nutritional adaptation. The transcriptomic response of L. garvieae to aeration level differed according to the presence or absence of S. aureus. The higher concentration of H₂O₂ with high aeration was not associated with a higher expression of L. garvieae H₂O₂-synthesis genes (pox, sodA, and spxA1) but rather with a repression of L. garvieae H₂O₂-degradation genes (trxB1, ahpC, ahpF, and gpx). We showed that L. garvieae displayed an original, previously undiscovered, H₂O₂ production regulation mechanism among bacteria. In addition to the key factor H₂O₂, the involvement of another extracellular effector in the antagonism against S. aureus was shown. Future studies should explore the relation between H₂O₂-metabolism, H₂O₂-producing LAB and the pathogen they inhibit. The nature of the other extracellular effector should also be determined.