Journal of Microbiology

Volume 50(6); December 2012

Research Support, Non-U.S. Gov'ts

Effects of Elevated CO2 and Pb on the Microbial Community in the Rhizosphere of Pinus densiflora: Sunghyun Kim , Sun Hwa Hong , Kyungsook Cho , Insook Lee , Gayoung Yoo , Hojeong Kang; J. Microbiol. 2012;50(6):895-901. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2207-1

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Abstract: Rising levels of atmospheric CO2 may stimulate forest productivity in the future, resulting in increased carbon storage in terrestrial ecosystems. However, heavy metal contamination may interfere with this, though the response is not yet known. In this study, we investigated the effect of elevated CO2 and Pb contamination on microorganisms and decomposition in pine tree forest soil. Three-year old pine trees (Pinus densiflora) were planted in Pb contaminated soils (500 mg/kg-soil) and uncontaminated soils and cultivated for three months in a growth chamber where the CO2 concentration was controlled at 380 or 760 mg/kg. Structures of the microbial community were comparatively analyzed in bulk and in rhizosphere soil samples using community-level physiological profiling (CLPP) and 16S rRNA gene PCRDGGE (denaturing gradient gel electrophoresis). Additionally, microbial activity in rhizospheric soil, growth and the C/N ratio of the pine trees were measured. Elevated CO2 significantly increased microbial activities and diversity in Pb contaminated soils due to the increase in carbon sources, and this increase was more distinctive in rhizospheric soil than in bulk soils. In addition, increased plant growth and C/N ratios of pine needles at elevated CO2 resulted in an increase in cation exchange capacity (CEC) and dissolved organic carbon (DOC) of the rhizosphere in Pb contaminated soil. Taken together, these findings indicate that elevated CO2 levels and heavy metals can affect the soil carbon cycle by changing the microbial community and plant metabolism.

Gibberellin-Producing Promicromonospora sp. SE188 Improves Solanum lycopersicum Plant Growth and Influences Endogenous Plant Hormones: Sang-Mo Kang , Abdul Latif Khan , Muhammad Hamayun , Javid Hussain , Gil-Jae Joo , Young-Hyun You , Jong-Guk Kim , In-Jung Lee; J. Microbiol. 2012;50(6):902-909. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2273-4

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Abstract: Plant growth-promoting rhizobacteria (PGPR) producing gibberellins (GAs) can be beneficial to plant growth and development. In the present study, we isolated and screened a new strain of Promicromonospora sp., SE188, isolated from soil. Promicromonospora sp. SE188 secreted GAs into its growth medium and exhibited phosphate solubilization potential. The PGPR produced physiologically active (GA1 and GA4) and inactive (GA9, GA12, GA19, GA20, GA24, GA34, and GA53) GAs in various quantities detected by GC/MS-SIM. Solanum lycopersicum (tomato) plants inoculated with Promicromonospora sp. SE188 showed a significantly higher shoot length and biomass as compared to controls where PGPR-free nutrient broth (NB) and distilled water (DW) were applied to plants. The presence of Promicromonospora sp. SE188 significantly up-regulated the non C-13 hydroxylation GA biosynthesis pathway (GA12→GA24→GA9→GA4→GA34) in the tomato plants as compared to the NB and DW control plants. Abscisic acid, a plant stress hormone, was significantly down-regulated in the presence of Promicromonospora sp. SE188. Contrarily, salicylic acid was significantly higher in the tomato plant after Promicromonospora sp. SE188 inoculation as compared to the controls. Promicromonospora sp. SE188 showed promising stimulation of tomato plant growth. From the results it appears that Promicromonospora sp. SE188 has potential as a bio-fertilizer and should be more broadly tested in field trials for higher crop production in eco-friendly farming systems.

Fungal Community Associated with Genetically Modified Poplar During Metal Phytoremediation: Moonsuk Hur , Young Woon Lim , Jae Jeong Yu , Se Uk Cheon , Young Im Choi , Seok-Hwan Yoon , Sang-Cheol Park , Dong-Il Kim , Hana Yi; J. Microbiol. 2012;50(6):910-915. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2491-9

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Abstract: Due to the increasing demand for phytoremediation, many transgenic poplars have been developed to enhance the bioremediation of heavy metals. However, structural changes to indigenous fungal communities by genetically modified organisms (GMO) presents a major ecological issue, due to the important role of fungi for plant growth in natural environments. To evaluate the effect of GM plant use on environmental fungal soil communities, extensive sequencing-based community analysis was conducted, while controlling the influence of plant clonality, plant age, soil condition, and harvesting season. The rhizosphere soils of GM and wild type (WT) poplars at a range of growth stages were sampled together with unplanted, contaminated soil, and the fungal community structures were investigated by pyrosequencing the D1/D2 region of the 28S rRNA gene. The results show that the overall structure of the rhizosphere fungal community was not significantly influenced by GM poplars. However, the presence of GM specific taxa, and faster rate of community change during poplar growth, appeared to be characteristic of the GM plant-induced effects on soil-born fungal communities. The results of this study provide additional information about the potential effects of GM poplar trees aged 1.5–3 years, on the soil fungal community.

Effects of Nutritional Input and Diesel Contamination on Soil Enzyme Activities and Microbial Communities in Antarctic Soils: Jiwon Han , Jaejoon Jung , Seunghun Hyun , Hyun Park , Woojun Park; J. Microbiol. 2012;50(6):916-924. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2636-x

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Abstract: Pollution of Antarctic soils may be attributable to increased nutritional input and diesel contamination via anthropogenic activities. To investigate the effect of these environmental changes on the Antarctic terrestrial ecosystem, soil enzyme activities and microbial communities in 3 types of Antarctic soils were evaluated. The activities of alkaline phosphomonoesterase and dehydrogenase were dramatically increased, whereas the activities of β-glucosidase, urease, arylsulfatase, and fluorescein diacetate hydrolysis were negligible. Alkaline phosphomonoesterase and dehydrogenase activities in the 3 types of soils increased 3- to 10-fold in response to nutritional input, but did not increase in the presence of diesel contamination. Consistent with the enzymatic activity data, increased copy numbers of the phoA gene, encoding an alkaline phosphomonoesterase, and the 16S rRNA gene were verified using quantitative real-time polymerase chain reaction. Interestingly, dehydrogenase activity and 16S rRNA gene copy number increased slightly after 30 days, even under diesel contamination, probably because of adaptation of the bacterial population. Intact Antarctic soils showed a predominance of Actinobacteria phylum (mostly Pseudonorcarida species) and other phyla such as Proteobacteria, Chloroflexi, Planctomycetes, Firmicutes, and Verrucomicrobia were present in successively lower proportions. Nutrient addition might act as a selective pressure on the bacterial community, resulting in the prevalence of Actinobacteria phylum (mostly Arthrobacter species). Soils contaminated by diesel showed a predominance of Proteobacteria phylum (mostly Phyllobacterium species), and other phyla such as Actinobacteria, Bacteroidetes, Planctomycetes, and Gemmatimonadetes were present in successively lower proportions. Our data reveal that nutritional input has a dramatic impact on bacterial communities in Antarctic soils and that diesel contamination is likely toxic to enzymes in this population.

Characterization, Metabolites and Gas Formation of Fumarate Reducing Bacteria Isolated from Korean Native Goat (Capra hircus coreanae): Lovelia L. Mamuad , Seon Ho Kim , Sung Sil Lee , Kwang Keun Cho , Che Ok Jeon , Sang-Suk Lee; J. Microbiol. 2012;50(6):925-931. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2497-3

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Abstract: Fumarate reducing bacteria, able to convert fumarate to succinate, are possible to use for the methane reduction in rumen because they can compete for H2 with methanogens. In this, we isolated fumarate reducing bacteria from a rumen of Korean native goat and characterized their molecular properties [fumarate reductase A gene (frdA)], fumarate reductase activities, and productions of volatile fatty acids and gas. Eight fumarate reducing bacteria belonging to Firmicutes were isolated from rumen fluid samples of slaughtered Korean black goats and characterized their phylogenetic positions based on 16S rRNA gene sequences. PCR based analyses showed that only one strain, closely related to Mitsuokella jalaludinii, harbored frdA. The growths of M. jalaludinii and Veillonella parvula strains were tested for different media. Interestingly, M. jalaludinii grew very well in the presence of hydrogen alone, while V. parvula grew well in response of fumarate and fumarate plus hydrogen. M. jalaludinii produced higher levels of lactate (P≤0.05) than did V. parvula. Additionally, M. jalaludinii produced acetate, but not butyrate, whereas V. parvula produced butyrate, not acetate. The fumarate reductase activities of M. jalaludinii and V. parvula were 16.8 ± 0.34 and 16.9 ± 1.21 mmol NADH oxidized/min/mg of cellular N, respectively. In conclusion, this showed that M. jalaludinii can be used as an efficient methane reducing agent in rumen.

DsbM, a Novel Disulfide Oxidoreductase Affects Aminoglycoside Resistance in Pseudomonas aeruginosa by OxyR-Regulated Response: Xuehan Wang , Mingxuan Li , Liwei Liu , Rui Mou , Xiuming Zhang , Yanling Bai , Haijin Xu , Mingqiang Qiao; J. Microbiol. 2012;50(6):932-938. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2177-3

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Abstract: A Pseudomonas aeruginosa mutant strain M122 was isolated from a Mu transposon insertion mutant library. In our prophase research, we have found that PA0058, a novel gene encodes a 234-residue conserved protein, was disrupted in the M122 mutant. In this study, the bacteriostatic experiment in vitro indicates that M122 has abnormally high aminoglycoside resistance. We expressed PA0058 in E. coli and found that PA0058 oxidizes and reduces disulfide. This biochemical characterization suggests that PA0058 is a novel disulfide oxidoreductase. Hence, the protein was designated as DsbM. Microarray analysis of the M122 mutant showed its unusual phenotype might be related to the bacterial antioxidant defense system mediated by the oxyR regulon. Meanwhile, we detected –SH content in the periplasm of M122 and wild strain and found a lower –SH/S–S ratio in M122. Therefore, we consider that the loss of dsbM function decreased the –SH/S–S ratio, which then prolongs the OxyR-regulated response, thereby conferring high aminoglycoside resistance to the M122 mutant strain. Our findings have important implications for understanding the mechanisms underlying aminoglycoside resistance in P. aeruginosa.

Characterization, Cloning, and Heterologous Expression of a Subtilisin-Like Serine Protease Gene VlPr1 from Verticillium lecanii: Gang Yu , Jin-Liang Liu , Li-Qin Xie , Xue-Liang Wang , Shi-Hong Zhang , Hong-Yu Pan; J. Microbiol. 2012;50(6):939-946. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2199-x

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Abstract: The entomopathogenic fungus Verticillium lecanii is a wellknown biocontrol agent. V. lecanii produces subtilisin-like serine protease (Pr1), which is important in the biological control activity of some insect pests by degrading insect cuticles. In this study, a subtilisin-like serine protease gene VlPr1 was cloned from the fungus and the VlPr1 protein was expressed in Escherichia coli. The VlPr1 gene contains an open reading frame (ORF) interrupted by three short introns, and encodes a protein of 379 amino acids. Protein sequence analysis revealed high homology with subtilisin serine proteases. The molecular mass of the protease was 38 kDa, and the serine protease exhibited its maximal activity at 40°C and pH 9.0. Protease activity was also affected by Mg2+ and Ca2+ concentration. The protease showed inhibitory activity against several plant pathogens, especially towards Fusarium moniliforme.

Quantification of Rice Brown Leaf Spot through Taqman Real-Time PCR Specific to the Unigene Encoding Cochliobolus miyabeanus SCYTALONE DEHYDRATASE1 Involved in Fungal Melanin Biosynthesis: Mukhamad Su’udi , Jong-Mi Park , Woo-Ri Kang , Sang-Ryeol Park , Duk-Ju Hwang , Il-Pyung Ahn; J. Microbiol. 2012;50(6):947-954. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2538-y

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Abstract: Rice brown leaf spot is a major disease in the rice paddy field. The causal agent Cochliobolus miyabeanus is an ascomycete fungus and a representative necrotrophic pathogen in the investigation of rice-microbe interactions. The aims of this research were to identify a quantitative evaluation method to determine the amount of C. miyabeanus proliferation in planta and determine the method’s sensitivity. Real-time polymerase chain reaction (PCR) was employed in combination with the primer pair and Taqman probe specific to CmSCD1, a C. miyabeanus unigene encoding SCYTALONE DEHYDRATASE, which is involved in fungal melanin biosynthesis. Comparative analysis of the nucleotide sequences of CmSCD1 from Korean strains with those from the Japanese and Taiwanese strains revealed some sequence differences. Based on the crossing point (CP) values from Taqman realtime PCR containing a series of increasing concentrations of cloned amplicon or fungal genomic DNA, linear regressions with a high level of reliability (R2>0.997) were constructed. This system was able to estimate fungal genomic DNA at the picogram level. The reliability of this equation was further confirmed using DNA samples from both resistant and susceptible cultivars infected with C. miyabeanus. In summary, our quantitative system is a powerful alternative in brown leaf spot forecasting and in the consistent evaluation of disease progression.

Genetic Organization and Conjugal Plasmid DNA Transfer of pHP69, a Plasmid from a Korean Isolate of Helicobacter pylori: Jung-Soo Joo , Jae-Young Song , Seung-Chul Baik , Woo-Kon Lee , Myung-Je Cho , Kon-Ho Lee , Hee-Shang Youn , Ji-Hyun Seo , Kwang-Ho Rhee , Hyung-Lyun Kang; J. Microbiol. 2012;50(6):955-961. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2580-9

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Abstract: We isolated pHP69, a 9,153 bp plasmid from Helicobacter pylori with a 33.98% (G+C) content. We identified 11 open reading frames (ORFs), including replication initiation protein A (repA), fic (cAMP-induced filamentation protein), mccC, mccB, mobA, mobD, mobB, and mobC, as well as four 22 bp tandem repeat sequences. The nucleic acid and predicted amino acid sequences of these ORFs exhibited significant homology to those of other H. pylori plasmids. pHP69 repA encodes a replication initiation protein and its amino acid sequence is similar to those of replicase proteins from theta-type plasmids. pHP69 contains two types of repeat sequences (R1 and R2), a MOBHEN family mobilization region comprising mobC, mobA, mobB, and mobD, and genes encoding microcin B and C. Among the 36 H. pylori strains containing plasmids, mobA or mccBC are present in 12 or 6, respectively and 3 contain both genes. To examine intrinsic capability of H. pylori for conjugative plasmid transfer, a shuttle vector pBHP69KH containing pHP69 and replication origin of pBR322 was constructed. It was shown that this vector could stably replicate and be mobilized among clinical H. pylori strains and demonstrated to gene transfer by natural plasmid.

Molecular Serotyping of Salmonella enterica by Complete rpoB Gene Sequencing: Won-Jin Seong , Hyuk-Joon Kwon , Tae-Eun Kim , Deog-Yong Lee , Mi-Sun Park , Jae-Hong Kim; J. Microbiol. 2012;50(6):962-969. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2547-x

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Abstract: Serotyping has been the gold standard for identifying Salmonella, but it requires large amounts of standard antisera. Multilocus sequence typing (MLST) has been applied to identify Salmonella serovars, but the recombination of 4–7 housekeeping genes and multiple analytic steps diminish its applicability. In the present study, we determined the complete sequences of the RNA polymerase beta subunit gene (rpoB) and 7 housekeeping genes (aroC, dnaN, hemD, hisD, purE, sucA, and thrA) for 76 strains of 33 Salmonella enterica serovars and conducted phylogenetic analyses together with the corresponding gene sequences of 24 reference strains registered in the GenBank database. Based on the phylogenetic analyses, 100 strains from 40 serovars and 91 strains from 37 serovars were classified into 60 rpoB (RST) and 49 multilocus sequence types (ST), respectively. The nucleotide similarities were 98.8–100% and 96.9–100% for the complete rpoB gene and the seven concatenated housekeeping genes, respectively. The strains of 35 and 30 serovars formed serovar-specific branches or clusters in the rpoB and housekeeping gene phylogenetic trees, respectively. Therefore, complete rpoB gene sequencing and phylogenetic analysis may be a useful method for identifying Salmonella serovars that is a simpler, more cost-effective, and less time-consuming alternative or complementary method to MLST and conventional serotyping.

Simultaneous Detection of Major Enteric Viruses Using a Combimatrix Microarray: Ju-Mi Kim , Sung Yeon Kim , Young Bin Park , Hye Jin Kim , Byung Sup Min , Jae-Chang Cho , Jai Myung Yang , You-Hee Cho , GwangPyo Ko; J. Microbiol. 2012;50(6):970-977. Published online October 27, 2012; DOI: https://doi.org/10.1007/s12275-012-2228-9

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Abstract: Various enteric viruses including norovirus, rotavirus, adenovirus, and astrovirus are the major etiological agents of food-borne and water-borne disease outbreaks and frequently cause non-bacterial gastroenteritis worldwide. Sensitive and high-throughput detection methods for these viral pathogens are compulsory for diagnosing viral pathogens and subsequently improving public health. Hence, we developed a sensitive, specific, and high-throughput analytical assay to detect most major enteric viral pathogens using “Combimatrix” platform oligonucleotide probes. In order to detect four different enteric viral pathogens in a sensitive and simultaneous manner, we first developed a multiplex RT-PCR assay targeting partial gene sequences of these viruses with fluorescent labeling for the subsequent microarray. Then, five olignonucleotides specific to each of the four major enteric viruses were selected for the microarray from the oligonulceotide pools targeting the specific genes obtained by multiplex PCR of these viruses. The oligonucleotide microarray was evaluated against stool specimens containing single or mixed viral species. As a result, we demonstrated that the multiplex RT-PCR assay specifically amplified partial sequences of four enteric viruses and the subsequent microarray assay was capable of sensitive and simultaneous detection of those viruses. The developed method could be useful for diagnosing enteric viruses in both clinical and environmental specimens.

Identification of Conserved Surface Proteins as Novel Antigenic Vaccine Candidates of Actinobacillus pleuropneumoniae: Xiabing Chen , Zhuofei Xu , Lu Li , Huanchun Chen , Rui Zhou; J. Microbiol. 2012;50(6):978-986. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2214-2

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Abstract: Actinobacillus pleuropneumoniae is an important swine respiratory pathogen causing great economic losses worldwide. Identification of conserved surface antigenic proteins is helpful for developing effective vaccines. In this study, a genome-wide strategy combined with bioinformatic and experimental approaches, was applied to discover and characterize surface-associated immunogenic proteins of A. pleuropneumoniae. Thirty nine genes encoding outer membrane proteins (OMPs) and lipoproteins were identified by comparative genomics and gene expression profiling as beinghighly conserved and stably transcribed in the different serotypes of A. pleuropneumoniae reference strains. Twelve of these conserved proteins were successfully expressed in Escherichia coli and their immunogenicity was estimated by homologous challenge in the mouse model, and then three of these proteins (APJL_0126, HbpA and OmpW) were further tested in the natural host (swine) by homologous and heterologous challenges. The results showed that these proteins could induce high titers of antibodies, but vaccination with each protein individually elicited low protective immunity against A. pleuropneumoniae. This study gives novel insights into immunogenicity of the conserved OMPs and lipoproteins of A. pleuropneumoniae. Although none of the surface proteins characterized in this study could individually induce effective protective immunity against A. pleuropneumoniae, they are potential candidates for subunit vaccines in combination with Apx toxins.

A New Quorum-Sensing Inhibitor Attenuates Virulence and Decreases Antibiotic Resistance in Pseudomonas aeruginosa: Yu-Xiang Yang , Zhen-Hua Xu , Yu-Qian Zhang , Jing Tian , Li-Xing Weng , Lian-Hui Wang; J. Microbiol. 2012;50(6):987-993. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2149-7

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Abstract: Quorum sensing (QS) has been a novel target for the treatment of infectious diseases. Here structural analogs of Pseudomonas aeruginosa autoinducer N-acyl homoserine lactone (AHL) were investigated for QS inhibitor (QSI) activity and a novel QSI was discovered, N-decanoyl-L-homoserine benzyl ester (C2). Virulence assays showed that C2 downregulated total protease and elastase activities, as well as the production of rhamnolipid, that are controlled by QS in P. aeruginosa wild-type strain PAO1 without affecting growth. C2 was also shown to inhibit swarming motility of PAO1. Using a microdilution checkerboard method, we identified synergistic interactions between C2 and several antibiotics, tobramycin, gentamycin, cefepime, and meropenem. Data from real-time RT-PCR suggested that C2 inhibited the expression of lasR (29.67%), lasI (21.57%), rhlR (28.20%), and rhlI (29.03%).

Catabolite Control Protein A of Streptococcus suis Type 2 Contributes to Sugar Metabolism and Virulence: Yulong Tang , Wei Wu , Xiaoyan Zhang , Zhongyan Lu , Jianshun Chen , Weihuan Fang; J. Microbiol. 2012;50(6):994-1002. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2035-3

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Abstract: Catabolite control protein A (CcpA) is the major transcriptional regulator in carbon catabolite repression in several Gram-positive bacteria. We attempted to characterize the role of a CcpA homologue of Streptococcus suis type 2 in sugar metabolism and virulence. Addition of glucose or sucrose to the defined medium significantly reduced the activity of raffinose-inducible α-galactosidase, cellobiose-inducible β-glucosidase, and maltose-inducible α-glucosidase of the wildtype strain by about 9, 4, and 2-3 fold, respectively. Deletion of ccpA substantially derepressed the effects of repressing sugars on α-galactosidase or β-glucosidase activity. The ccpA deletion mutant showed reduced expression of virulence genes sly and eno (P<0.05), decreased adhesion to and invasion into endothelial cells (P<0.05), and attenuated virulence to mice with significant reduction of death rate and bacterial burden in organs, as compared to the wild-type strain. Both the in vitro and in vivo defect phenotypes were reversible by ccpA complementation. Thus, this study shows that CcpA of S. suis type 2 plays an important role in carbon catabolite repression and virulence.

Immunoprophylactic Effects of Shiitake Mushroom (Lentinula edodes) against Bordetella bronchiseptica in Mice: Bock-Gie Jung , Jin-A Lee , Bong-Joo Lee; J. Microbiol. 2012;50(6):1003-1008. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2365-1

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Abstract: Antimicrobials are used as feed additives to improve growth performance and to prevent subclinical disease challenge in industrial animals. However, these drugs can lead to the development of resistant strains of bacteria. Shiitake mushrooms (SM) (Lentinula edodes) have long been popular as a health food in East Asia. Moreover, SM-derived polysaccharides are well-known as immunostimulants that possess antimicrobial properties. The aim of the present study was to evaluate the immunoprophylactic effects of SM against Bordetella bronchiseptica infection in mice as an initial step towards the development of eco-friendly feed additives to reduce the use of antimicrobials. Although SM had no effect on body weight gain under the un-infected conditions, SM alleviated progressive weight loss and helped in the recovery of body weight in B. bronchiseptica infected mice. Dietary supplementation with SM reinforced bacterial clearance in the infected mice. Of note, SM markedly increased the percentage of various T lymphocytes and the relative mRNA expression levels of tumor necrosis factor-α and interferon-γ in the bronchial lymph node early in the infection. Taken together, these findings suggest that SM could help in the improvement of body weight gain during B. bronchiseptica infection and may enhance the protective immune activity against a subclinical disease challenge, such as B. bronchiseptica infection in mice, probably by a strong stimulation of non-specific immune responses. Hence, SM may provide an alternative to reduce use of antimicrobials. Confirmation of the beneficial effects of SM as a feed additive is now required in industrial animals.

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