The authors wish to thank the EEA Grant NILS Science and Sustainability Coordinated Mobility of Researchers (reference 017-ABEL-CM-2013). C.B. and G.P.-M. were supported by the AGL2015-70487-P grant from the Spanish Ministry of Economy and Competitiveness. O.C.O.U. and D.B.D. were supported by a strategic scholarship program for food science research from the Norwegian University of Life Sciences (NMBU) (project 1205051025). We would also like to thank Inmaculada Noguera for her assistance with animal care and sampling and Jesus Dehesa for his help with ensuring the availability of laboratory materials in the animal facility. We also appreciate Professor Lars-Gustav Snipen for his advice on statistics.

Care and handling must be carried out at a specialized animal care unit. Procedures described here were approved by the corresponding Ethics Committee of the University of Valencia and local authorities, following the principles of laboratory animal care mandatory by European Union Law and 2010/63/EU and the Spanish Government RD 53/2013 on the protection of animals used for scientific purposes, in order to respect the 3R principle in animal experimentation (Replacement, Reduction, Refinement).
...

<ol>
	<li>Papagianni, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ribosomally+synthesized+peptides+with+antimicrobial+properties:+biosynthesis,+structure,+function,+and+applications.">Ribosomally synthesized peptides with antimicrobial properties: biosynthesis, structure, function, and applications.</a> Biotechnol Adv. 21 (6), 465-499 (2003).</li><li>Gillor, O., Kirkup, B. C., Riley, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Advances in Applied Microbiology. 54, 129-146 (2004).</li><li>Dzung, B. D., Ingolf, F. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ribosomally+Synthesized+Antibacterial+Peptides+in+Gram+Positive+Bacteria.">Ribosomally Synthesized Antibacterial Peptides in Gram Positive Bacteria.</a> Curr Drug Targets. 3 (2), 107-122 (2002).</li><li>Dobson, A., Cotter, P. D., Ross, R. P., Hill, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bacteriocin+Production:+a+Probiotic+Trait?.">Bacteriocin Production: a Probiotic Trait?.</a> Appl Environ Microb. 78 (1), 1-6 (2012).</li><li>Li, D., Wang, P., Wang, P., Hu, X., Chen, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+gut+microbiota:+A+treasure+for+human+health.">The gut microbiota: A treasure for human health.</a> Biotechnol Adv. 34 (7), 1210-1224 (2016).</li><li>Millette, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Capacity+of+Human+Nisin-+and+Pediocin-Producing+Lactic+Acid+Bacteria+To+Reduce+Intestinal+Colonization+by+Vancomycin-Resistant+Enterococci.">Capacity of Human Nisin- and Pediocin-Producing Lactic Acid Bacteria To Reduce Intestinal Colonization by Vancomycin-Resistant Enterococci.</a> Appl Environ Microb. 74 (7), 1997-2003 (2008).</li><li>Cotter, P. D., Ross, R. P., Hill, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bacteriocins+[mdash]+a+viable+alternative+to+antibiotics?.">Bacteriocins [mdash] a viable alternative to antibiotics?.</a> Nat Rev Microb. 11 (2), 95-105 (2013).</li><li>Leroy, F., Foulqui&#233; Moreno, M. R., De Vuyst, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enterococcus+faecium+RZS+C5,+an+interesting+bacteriocin+producer+to+be+used+as+a+co-culture+in+food+fermentation.">Enterococcus faecium RZS C5, an interesting bacteriocin producer to be used as a co-culture in food fermentation.</a> Int J Food Microb. 88 (2-3), 235-240 (2003).</li><li>Ananou, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Combined+effect+of+enterocin+AS-48+and+high+hydrostatic+pressure+to+control+food-borne+pathogens+inoculated+in+low+acid+fermented+sausages.">Combined effect of enterocin AS-48 and high hydrostatic pressure to control food-borne pathogens inoculated in low acid fermented sausages.</a> Meat Sci. 84 (4), 594-600 (2010).</li><li>Riboulet-Bisson, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+Lactobacillus+salivarius+Bacteriocin+Abp118+on+the+Mouse+and+Pig+Intestinal+Microbiota.">Effect of Lactobacillus salivarius Bacteriocin Abp118 on the Mouse and Pig Intestinal Microbiota.</a> PLoS One. 7 (2), e31113 (2012).</li><li>Charan, J., Kantharia, N. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=How+to+calculate+sample+size+in+animal+studies?.">How to calculate sample size in animal studies?.</a> J Pharmacol Pharmacother. 4 (4), 303-306 (2013).</li><li>Umu, &. #. 2. 1. 4. ;. C. O., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Potential+of+Class+II+Bacteriocins+to+Modify+Gut+Microbiota+to+Improve+Host+Health.">The Potential of Class II Bacteriocins to Modify Gut Microbiota to Improve Host Health.</a> PLoS One. 11 (10), e0164036 (2016).</li><li>Edgar, R. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=UPARSE:+highly+accurate+OTU+sequences+from+microbial+amplicon+reads.">UPARSE: highly accurate OTU sequences from microbial amplicon reads.</a> Nat Meth. 10 (10), 996-998 (2013).</li><li>Edgar, R. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Search+and+clustering+orders+of+magnitude+faster+than+BLAST.">Search and clustering orders of magnitude faster than BLAST.</a> Bioinformatics. 26 (19), 2460-2461 (2010).</li><li>Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., Knight, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=UCHIME+improves+sensitivity+and+speed+of+chimera+detection.">UCHIME improves sensitivity and speed of chimera detection.</a> Bioinformatics. 27 (16), 2194-2200 (2011).</li><li>Caporaso, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=QIIME+allows+analysis+of+high-throughput+community+sequencing+data.">QIIME allows analysis of high-throughput community sequencing data.</a> Nat Meth. 7 (5), 335-336 (2010).</li><li>DeSantis, T. Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Greengenes,+a+Chimera-Checked+16S+rRNA+Gene+Database+and+Workbench+Compatible+with+ARB.">Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB.</a> Appl Environ Microb. 72 (7), 5069-5072 (2006).</li><li>Caporaso, J. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PyNAST:+a+flexible+tool+for+aligning+sequences+to+a+template+alignment.">PyNAST: a flexible tool for aligning sequences to a template alignment.</a> Bioinformatics. 26 (2), 266-267 (2010).</li><li>Wang, Q., Garrity, G. M., Tiedje, J. M., Cole, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Naive+Bayesian+Classifier+for+Rapid+Assignment+of+rRNA+Sequences+into+the+New+Bacterial+Taxonomy.">Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy.</a> Appl Environ Microb. 73 (16), 5261-5267 (2007).</li><li>Price, M. N., Dehal, P. S., Arkin, A. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FastTree+2+-+Approximately+Maximum-Likelihood+Trees+for+Large+Alignments.">FastTree 2 - Approximately Maximum-Likelihood Trees for Large Alignments.</a> PLoS One. 5 (3), e9490 (2010).</li><li>Lozupone, C., Knight, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=UniFrac:+a+New+Phylogenetic+Method+for+Comparing+Microbial+Communities.">UniFrac: a New Phylogenetic Method for Comparing Microbial Communities.</a> Appl Environ Microb. 71 (12), 8228-8235 (2005).</li><li>Faust, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microbial+co-occurrence+relationships+in+the+human+microbiome.">Microbial co-occurrence relationships in the human microbiome.</a> PLoS Comput Biol. 8 (7), e1002606 (2012).</li><li>Shannon, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cytoscape:+A+Software+Environment+for+Integrated+Models+of+Biomolecular+Interaction+Networks.">Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks.</a> Genome Res. 13 (11), 2498-2504 (2003).</li><li>Klindworth, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+of+general+16S+ribosomal+RNA+gene+PCR+primers+for+classical+and+next-generation+sequencing-based+diversity+studies.">Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies.</a> Nucleic Acids Res. 41 (1), e1 (2013).</li><li>Edwards, A. N., Su&#225;rez, J. M., McBride, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Culturing+and+Maintaining+Clostridium+difficile+in+an+Anaerobic+Environment.">Culturing and Maintaining Clostridium difficile in an Anaerobic Environment.</a> J Vis Exp. (79), e50787 (2013).</li><li>Delves-Broughton, J., Blackburn, P., Evans, R. J., Hugenholtz, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Applications+of+the+bacteriocin,+nisin.">Applications of the bacteriocin, nisin.</a> Antonie Van Leeuwenhoek. 69 (2), 193-202 (1996).</li><li>Allende, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Growth+and+bacteriocin+production+by+lactic+acid+bacteria+in+vegetable+broth+and+their+effectiveness+at+reducing+Listeria+monocytogenes+in+vitro+and+in+fresh-cut+lettuce.">Growth and bacteriocin production by lactic acid bacteria in vegetable broth and their effectiveness at reducing Listeria monocytogenes in vitro and in fresh-cut lettuce.</a> Food Microb. 24 (7-8), 759-766 (2007).</li><li>Strompfov&#225;, V., Laukov&#225;, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vitro+study+on+bacteriocin+production+of+Enterococci+associated+with+chickens.">In vitro study on bacteriocin production of Enterococci associated with chickens.</a> Anaerobe. 13 (5-6), 228-237 (2007).</li><li>Caballero-Guerrero, B., Jim&#233;nez D&#237;az, R., Maldonado-Barrag&#225;n, A., Ruiz-Barba, J. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coculture+with+specific+bacteria+enhances+survival+of+Lactobacillus+plantarum+NC8,+an+autoinducer-regulated+bacteriocin+producer,+in+olive+fermentations.">Coculture with specific bacteria enhances survival of Lactobacillus plantarum NC8, an autoinducer-regulated bacteriocin producer, in olive fermentations.</a> Food Microb. 27 (3), 413-417 (2010).</li><li>Drider, D., Fimland, G., H&#233;chard, Y., McMullen, L. M., Pr&#233;vost, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Continuing+Story+of+Class+IIa+Bacteriocins.">The Continuing Story of Class IIa Bacteriocins.</a> Microb. Mol Biol Rev. 70 (2), 564-582 (2006).</li><li>Gao, Y., Jia, S., Gao, Q., Tan, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+bacteriocin+with+a+broad+inhibitory+spectrum+produced+by+Lactobacillus+sake+C2,+isolated+from+traditional+Chinese+fermented+cabbage.">A novel bacteriocin with a broad inhibitory spectrum produced by Lactobacillus sake C2, isolated from traditional Chinese fermented cabbage.</a> Food Control. 21 (1), 76-81 (2010).</li></ol>

The procedure described here has been used to determine whether changes in the microbiota are bound to health or age. Different parts of the protocol are important, but among them, sampling the feces, choosing the DNA fragment to be sequenced and analyzed, and performing the DNA extraction and bioinformatic analysis could certainly be the most critical points. Sampling is crucial because, for ethical reasons, mice should not be stressed and because it is known to change the proportion of bacteria in the gut. Samples must...

Bacteriocins are antimicrobial peptides produced by a wide range of bacterial species1,2. These compounds and their producers, especially LAB, have been explored and exploited worldwide for decades for their potential applications in food preservation and medicine3. Several bacteriocins are known to kill important pathogens, including species of Listeria, Enterococcus, Staphylococcus, and Bacillus. Some bacteriocins even have the ability to modulate the immune response4. Many bacteriocins have relatively narrow spectra, a property that is much appreciated in some applications. For example, some narrow-spectrum bacteriocins can be used to direct specific activity against selected groups of problematic bacteria, without much disturbance on the commensal or beneficial flora sharing the same niche; this is especially essential in the gut environment, where numerous beneficial microbes thrive in an interactive and dynamic manner5. Bacteriocins are also very attractive for prophylactic or probiotic use, as they can suppress the (out)growth of pathogens, pathobionts, or opportunistic bacteria that may unbalance the gut homeostasis6,7.
In terms of their nature and physicochemical properties, bacteriocins are very diverse, as they have different structures, target specificities, modes of action, etc. Most bacteriocins have been studied in great detail in in vitro settings, but very few have been tested in food matrices8,9 or in vivo, such as in an animal gut6,10. The in vitro properties can differ to a great extent when assessed in vivo due to the complexity of the gut environment and also to putative unintended effects on beneficial bacteria. Most probiotics are LAB. They produce an array of other metabolites, including short-chain fatty acids, which are known to influence the physiology of the host, as well as to demonstrate antimicrobial properties toward certain bacteria. Therefore, in the case of probiotic strains that produce bacteriocins, it is best to establish realistic assays, such as healthy animals with normal microbiota.
In the present study, we provide a strategy that allows for the assessment of the effect of different bacteriocin-producing strains, whose bacteriocins have different inhibitory spectra, on healthy mice. Our strategy includes feeding mice with isogenic non-bacteriocin mutants, which enables the differentiation of bacteriocin-mediated effects from non-bacteriocin-mediated effects. Sequencing 16S rDNA allows for following the dynamic changes of the bacterial population in the gut. Subsequent statistical analysis deciphers correlations between bacterial species and also between bacterial species and measured physiological parameters (e.g., bodyweight, serum biochemical parameters, etc.). We believe that the protocol presented in this study is also applicable to other probiotic or prebiotic applications beyond the study of bacteriocins in live animals.

<table border="0" cellpadding="0" cellspacing="0" width="826">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Balb/c mice (female)</td>
			<td style="width:141px;">Harlan</td>
			<td style="width:183px;"></td>
			<td style="width:287px;">Mice should be 6 - 8 weeks of age</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Plastic Petri dish</td>
			<td style="width:141px;">Thermo Scientific</td>
			<td style="width:183px;">101VR20</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Brain-Heart-Infusion broth</td>
			<td style="width:141px;">Conda</td>
			<td style="width:183px;">1400.00</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">European Bacteriological Agar</td>
			<td style="width:141px;">Pronadisa</td>
			<td style="width:183px;">1800.00</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Agarose D1 Low EEO</td>
			<td style="width:141px;">Pronadisa</td>
			<td style="width:183px;">8010.00</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">1XTAE buffer</td>
			<td style="width:141px;">Thermo Scientific</td>
			<td style="width:183px;">15558042</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">MRS broth</td>
			<td style="width:141px;">Difco</td>
			<td style="width:183px;">288130</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">PBS tablets</td>
			<td style="width:141px;">Sigma</td>
			<td style="width:183px;">P4417-100TAB</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">scale</td>
			<td style="width:141px;">Mettler Toledo</td>
			<td style="width:183px;">PB602-S</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">sterile forceps</td>
			<td style="width:141px;">Levantina de Laboratorios S.L.</td>
			<td style="width:183px;">260-3710014</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Microcentrifuge</td>
			<td style="width:141px;">Eppendorf</td>
			<td style="width:183px;">5424</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Centrifuge</td>
			<td style="width:141px;">Hermle</td>
			<td style="width:183px;">Z383K</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">sodium chloride</td>
			<td style="width:141px;">AppliChem Panreac</td>
			<td style="width:183px;">121659.1211</td>
			<td></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Realpure SSS Kit</td>
			<td style="width:141px;">Real Life Science Solutions, Durviz, Spain</td>
			<td style="width:183px;">RBME04 (300 ml)</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Isopropanol</td>
			<td style="width:141px;">AppliChem Panreac</td>
			<td style="width:183px;">131090.1611</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Ethanol</td>
			<td style="width:141px;">AppliChem Panreac</td>
			<td style="width:183px;">131086.1214</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Qubit fluorometer</td>
			<td style="width:141px;">Invitrogen</td>
			<td style="width:183px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Qubit dsDNA HS Assay Kit</td>
			<td style="width:141px;">Invitrogen</td>
			<td style="width:183px;">Q32851</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">AMPure XP beads</td>
			<td style="width:141px;">Beckman Coulter Genomics, USA</td>
			<td style="width:183px;">A63881 (60 ml)</td>
			<td></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">PerfeCta NGS library quantification kit</td>
			<td style="width:141px;">Quanta BioSciences, Maryland, USA</td>
			<td style="width:183px;">733-2300</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">MiSeq v3 reagent kit</td>
			<td style="width:141px;">Illumina, San Diego, California, USA</td>
			<td style="width:183px;">MS-102-3003</td>
			<td></td>
		</tr>
		<tr height="147">
			<td height="147" style="height:147px;width:216px;">Primers for 16S rRNA gene amplification</td>
			<td style="width:141px;"></td>
			<td style="width:183px;"></td>
			<td style="width:287px;">Primers contain V3-V4 region of bacterial 16S rRNA gene and Illumina overhang adaptors:5&#8217;-TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CCT ACG GGN GGC WGC AG-3&#8217; and 5&#39;-GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGA CTA CHV GGG TAT CTA ATC C-3&#8217;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Nextera XT Index kit</td>
			<td style="width:141px;"></td>
			<td style="width:183px;">FC-131-1002</td>
			<td>Indices and Illumina sequencing adaptors</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Micropestle for 1.5 ml tubes, Eppendorf / Sigma , Ref.</td>
			<td style="width:141px;">Sigma</td>
			<td style="width:183px;">Z317314-1PAK</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Glass beads, 0.1 mm diameter</td>
			<td style="width:141px;">Biospec Products</td>
			<td style="width:183px;">11079-101</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">NucleoSpin Gel and PCR Clean-up Kit</td>
			<td style="width:141px;">Macherey-Nagel</td>
			<td style="width:183px;">740609.25</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Omni Bead Ruptor 24</td>
			<td style="width:141px;">Omni International Inc.</td>
			<td style="width:183px;">19-040</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">mutanolysin</td>
			<td style="width:141px;">Sigma</td>
			<td style="width:183px;">M9901-10KU</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">lysozyme</td>
			<td style="width:141px;">Roche</td>
			<td style="width:183px;">10837059001</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">proteinase K</td>
			<td style="width:141px;">Roche</td>
			<td style="width:183px;">3115887001</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Rnase A</td>
			<td style="width:141px;">Sigma</td>
			<td style="width:183px;">R4875</td>
			<td></td>
		</tr>
	</tbody>
</table>

a method to assess bacteriocin effects on the gut microbiota of mice

Very intriguing questions arise with our advancing knowledge on gut microbiota composition and the relationship with health, particularly relating to the factors that contribute to maintaining the population balance. However, there are limited available methodologies to evaluate these factors. Bacteriocins are antimicrobial peptides produced by many bacteria that may confer a competitive advantage for food acquisition and/or niche establishment. Many probiotic lactic acid bacteria (LAB) strains have great potential to promote human and animal health by preventing the growth of pathogens. They can also be used for immuno-modulation, as they produce bacteriocins. However, the antagonistic activity of bacteriocins is normally determined by laboratory bioassays under well-defined but over-simplified conditions compared to the complex gut environment in humans and animals, where bacteria face multifactorial influences from the host and hundreds of microbial species sharing the same niche. This work describes a complete and efficient procedure to assess the effect of a variety of bacteriocins with different target specificities in a murine system. Changes in the microbiota composition during the bacteriocin treatment are monitored using compositional 16S rDNA sequencing. Our approach uses both the bacteriocin producers and their isogenic non-bacteriocin-producing mutants, the latter giving the ability to distinguish bacteriocin-related from non-bacteriocin-related modifications of the microbiota. The fecal DNA extraction and 16S rDNA sequencing methods are consistent and, together with the bioinformatics, constitute a powerful procedure to find faint changes in the bacterial profiles and to establish correlations, in terms of cholesterol and triglyceride concentration, between bacterial populations and health markers. Our protocol is generic and can thus be used to study other compounds or nutrients with the potential to alter the host microbiota composition, either when studying toxicity or beneficial effects.

The production of bacteriocins has been considered a positive probiotic feature in LAB, as it was assumed to prevent the growth of opportunistic bacteria and pathogens. The aim of this work was to show the capacity of bacteriocins to modulate gut microbiota populations in a mouse model. For this purpose, a procedure was developed to compare the effect of the intake of bacteriocin-producing strains and their isogenic non-producing strains. The procedure for the inoculation and the time ext...

Watch this Scientific Journal Video about A Method to Assess Bacteriocin Effects on the Gut Microbiota of Mice at JoVE.com

A Method to Assess Bacteriocin Effects on the Gut Microbiota of Mice

Bacteriocins are believed to play a key role in defining microbial diversity in different ecological niches. Here, we describe an efficient procedure to assess how bacteriocins affect gut microbiota composition in an animal model.

Very intriguing questions arise with our advancing knowledge on gut microbiota composition and the relationship with health, particularly relating to the ...

The overall goal of this procedure is to assess the influence of bacteriocins on gut microbiota composition using a mouse model. This method will help determine the real effect of bacteriocins from probiotics on the delicate balance of bacterial populations in the gut. The main advantage of this technique is that it allows the analysis of physiological parameters to infer global effects on the host organism.After growing bacterial cultures according to the text protocol, count the cells by first using ice-cold, 0.9%sodium chloride solution to make ten fold serial dilutions. Spread 100 microliters of each dilution onto a BHI Agar plate. Incubate the plates at 30 degrees Celsius overnight for cell growth and colony formation to determine the CFU per milliliter.To prepare bacteria-containing drinking water, use 100 milliliters of sterile, filtered drinking water to dilute the cells from each bacterial stock culture for a final average of ten to the ninth per milliliter CFU. For bacterial survival assessment, count live cells just after dilution and after 24 hours once a week during the first two weeks of bacteria treatment. After ear labeling and acclimating BALB/c young female mice according to the text protocol, on day one of the experiment, collect fecal samples for each mouse and mark them as time zero, or t zero.Place the samples in previously prepared storage boxes and refrigerate the samples at four degrees Celsius until their transport to the laboratory, where they'll be frozen at minus 80 degrees Celsius, then weigh the mice and record the weight. Prepare bacteria-containing drinking water as demonstrated earlier in the video and place drinking water bottles in the corresponding independent cages that are clearly identified so that the mice in each cage share the same water bottle. Prepare new bottles with 100 milliliters of fresh drinking water every day for 15 days preferably using mineral water to avoid chlorine or bacterial inhibiting compounds, and add freshly defrosted bacterial suspensions.Collect fecal samples on days seven and 14. Then, for the next two weeks, allow the mice to drink bacteria-free water and collect additional fecal samples on days 21 and 28. To count bacteriocin-producing bacteria cells in fecal samples, transfer diluted cells of the bacteriocin producer to four milliliters of pre-warmed MRS soft agar.Mix the agar by vortexing and pour the cells onto an MRS 1.5%agar plate. This layer is referred to as the first layer. Transfer another four milliliters of cell-free 0.8%MRS soft agar onto the first layer to embed all the cells within the soft agar.This layer is meant to prevent cells from growing as colonies on the surface of the agar plates. In the sterile hood, dry the plates by taking the lid off for five to 10 minutes before incubating the plates at 30 degrees Celsius for 20 to 24 hours for cell growth and colony formation. To identify bacteriocin producing colonies, mix 40 microliters of an overnight culture of an appropriate indicator strain with four milliliters of pre-warmed soft agar for each plate.Pour the mixture onto the plates. This layer is referred to as the third layer. Dry and incubate the plates as before for cell growth and colony formation.Bacteriocin-producing colonies have clear zones of inhibition around the colonies. Using a commercial DNA extraction kit, suspend one to two fecal mice pellets in 300 microliters of re-suspension solution. Transfer the sample to a two milliliter microtube with 0.5 grams of glass beads.Add one microliter of 10 units per microliter Mutanolysin and two microliters of 20 milligrams per milliliter Lysozyme to each sample and incubate the tubes at 37 degrees Celsius for 40 to 60 minutes. Disrupt the samples using vibration and glass beads, and then proceed with one of the standard protocols for DNA extraction from fecal samples. After isolating and cleaning the DNA according to the text protocol, quantify the samples.Then, normalize and pool each sample from mice sharing the same cage at each time point. The aim of this work was to show the capacity of bacteriocins to modulate gut microbiota populations in a mouse model. The tested bacteriocin-producing lactic acid bacteria, or LAB, as well as the respective counts in drinking water and counts in feces are summarized here.An example of the bacteriocin production by LAB recovered from feces is illustrated in this figure. This PCoA plot reveals that there were no significant differences between the bacteriocin treatments and the isogenic strains when all samples and all bacteria groups were considered together. However, there were likely differences when particular bacterial genera were studied independently, as shown here where changes in the relative abundances of genera were compared to the control group.Furthermore, Pearson's correlation analysis revealed significant linkage between different bacterial genera and a correlation between bacterial genera and triglycerides and LDL in serum, as shown by this network built in CoNet. While attempting this procedure, it's important to remember the use of isogenic strains as controls and a control without bacterial treatment. Following this procedure, other methods like hepatic function, moe-coe-sic transcriptomics, and fecal water metabolomics can be performed and all at once while additional questions, like how do microbiota fluctuations affect the bile salts, cholesterol cycle, digestibility of nutrients, and immune response.

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14.1K Aufrufe.  Consejo Superior de Investigaciones Científicas (CSIC). The overall goal of this procedure is to assess the influence of bacteriocins on gut microbiota composition using a mouse model. This method will help determine the real effect of bacteriocins from probiotics on the delicate balance of bacterial populations in the gut. The main advantage of this technique is that it allows the analysis of physiological parameters to infer global effects on the host organism.After growing bacterial cultures according to the text protocol, count the cell...