Biochemical and Molecular Characterization of Obesumbacterium proteus , a Common Contaminant of Brewing Yeasts

Intrinsic Resistance to Colistin in the Genus Hafnia

A bacterial species is considered to be intrinsically resistant to an antimicrobial when nearly all of the wild-type isolates (i.e., those without acquired resistance) exhibit minimum inhibitory concentration (MIC) values that are sufficiently high such that susceptibility testing is unnecessary, and that the antimicrobial should not be considered for therapy. Accordingly, knowledge of intrinsic resistance influences both the selection of treatment regimens and the approach to susceptibility testing in the clinical laboratory, where unexpected results also facilitate the recognition of microbial identification or susceptibility testing errors. Previously, limited data have suggested that Hafnia spp. may be intrinsically resistant to colistin. We evaluated the in vitro activity of colistin against 119 Hafniaceae that were isolated from human samples: 75 (63%) from routine clinical cultures and 44 (37%) from stool samples of travelers undergoing screening for antimicrobial resistant organisms. Broth microdilution colistin MICs were ≥4 μg/mL for 117 of 119 (98%) isolates. Whole-genome sequencing of 96 of the isolates demonstrated that the colistin-resistant phenotype was not lineage-specific. 2 of the 96 (2%) isolates harbored mobile colistin resistance genes. Compared to whole-genome sequencing, VITEK MS matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and VITEK 2 GN ID failed to consistently distinguish between Hafnia alvei, Hafnia paralvei, and Obesumbacterium proteus. In conclusion, using a reference antimicrobial susceptibility testing method and a genetically diverse collection of isolates, we found Hafnia spp. to be intrinsically resistant to colistin. The recognition of this phenotype will help inform rational approaches by which to perform antimicrobial susceptibility testing and therapy for patients with infections that are caused by Hafnia spp.

Overview of craft brewing specificities and potentially associated microbiota

The brewing process differs slightly in craft breweries as compared to industrial breweries, as there are fewer control points. This affects the microbiota of the final product. Beer contains several antimicrobial properties that protect it from pathogens, such as low pH, low oxygen and high carbon dioxide content, and the addition of hops. However, these hurdles have limited power controlling spoilage organisms. Contamination by these organisms can originate in the raw materials, persist in the environment, and be introduced by using flavoring ingredients later in the process. Spoilage is a prominent issue in brewing, and can cause quality degradation resulting in consumer rejection and product waste. For example, lactic acid bacteria are predominately associated with producing a ropy texture and haze, along with producing diacetyl which gives the beer butter flavor notes. Other microorganisms may not affect flavor or aroma, but can retard fermentation by consuming nutrients needed by fermentation yeast. Quality control in craft breweries today relies on culturing methods to detect specific spoilage organisms. Using media can be beneficial for detecting the most common beer spoilers, such as Lactobacillus and Pediococci. However, these methods are time consuming with long incubation periods. Molecular methods such as community profiling or high throughput sequencing are better used for identifying entire populations of beer. These methods allow for detection, differentiation, and identification of taxa.

Biogenic hydrogen and methane production from Chlorella vulgaris and Dunaliella tertiolecta biomass

BACKGROUND

Microalgae are a promising feedstock for biofuel and bioenergy production due to their high photosynthetic efficiencies, high growth rates and no need for external organic carbon supply. In this study, utilization of Chlorella vulgaris (a fresh water microalga) and Dunaliella tertiolecta (a marine microalga) biomass was tested as a feedstock for anaerobic H2 and CH4 production.

RESULTS

Anaerobic serum bottle assays were conducted at 37°C with enrichment cultures derived from municipal anaerobic digester sludge. Low levels of H2 were produced by anaerobic enrichment cultures, but H2 was subsequently consumed even in the presence of 2-bromoethanesulfonic acid, an inhibitor of methanogens. Without inoculation, algal biomass still produced H2 due to the activities of satellite bacteria associated with algal cultures. CH4 was produced from both types of biomass with anaerobic enrichments. Polymerase chain reaction-denaturing gradient gel electrophoresis profiling indicated the presence of H2-producing and H2-consuming bacteria in the anaerobic enrichment cultures and the presence of H2-producing bacteria among the satellite bacteria in both sources of algal biomass.

CONCLUSIONS

H2 production by the satellite bacteria was comparable from D. tertiolecta (12.6 ml H2/g volatile solids (VS)) and from C. vulgaris (10.8 ml H2/g VS), whereas CH4 production was significantly higher from C. vulgaris (286 ml/g VS) than from D. tertiolecta (24 ml/g VS). The high salinity of the D. tertiolecta slurry, prohibitive to methanogens, was the probable reason for lower CH4 production.

Gram-negative bacteria associated with brewery yeasts: reclassification of Obesumbacterium proteus biogroup 2 as Shimwellia pseudoproteus gen. nov., sp. nov., and transfer of Escherichia blattae to Shimwellia blattae comb. nov

Phylogenetic analyses of type and reference strains of Obesumbacterium proteus biogroups 1 and 2 plus a novel isolate of biogroup 2 were carried out based on 16S rRNA gene sequences and partial sequences of four protein-coding genes (fusA, leuS, pyrG and rpoB). Both approaches revealed that O. proteus biogroup 1 strains were closely related to Hafnia alvei. Biogroup 2 strains, however, formed a distinct monophyletic clade of generic status that included Escherichia blattae. Phenotypic tests were consistent with the molecular classification and provided diagnostic features. It is proposed that biogroup 2 strains be placed in a new genus, Shimwellia gen. nov., as Shimwellia pseudoproteus sp. nov., with strain 521T (=DSM 3038T=LMG 24835T=NCIMB 14534T) as the type strain, and that Escherichia blattae be transferred to the genus Shimwellia as Shimwellia blattae comb. nov., with strain ATCC 29907T (=DSM 4481T) as the type strain.

Binding of nontarget microorganisms from food washes to anti-Salmonella and anti-E. coli O157 immunomagnetic beads: most probable composition of background Eubacteria

We present herein the composition of bacterial communities occurring in ground chicken and the changes which arise in these populations based upon nonselective partitioning by commercially-available Dynal anti-Salmonella and anti-E. coli O157 immunomagnetic beads (IMB). Our enumeration and colony selection protocol was based upon a 6 × 6 drop plate method (n = 18 for each 25-g sub-sampling) using a dilution which resulted in ca. 4-8 colonies per drop. An average of 82 ± 13 colonies were selected from three 25-g ground chicken subsamplings per batch, each of which was repeated seasonally for one year. DNA was extracted from each colony and the composition of Eubacteria in each of these harvests was determined by sequence-based identification of 16S rDNA amplicons. The Gram-positive bacteria Brochothrix thermosphacta and Carnobacterium maltaromticum were the most commonly found organisms in both the total chicken wash (PBS) and in the IMB-bound (PBS-washed) fractions. The remaining background organisms which also adhered to varying degrees to commercial IMBs were: Pseudomonas oleovorans, Acinetobacter lwoffi, Serratia spp., and one Rahnella spp. A large number of the organisms were also cladistically evaluated based on rDNA basepair disparities: all Brochothrices were monophyletic; twelve different Pseudomonads were found along with eight Carnobacteria, seven Acinetobacteres, four Serratiae, and two Rahnellae. Carnobacterium alone showed an IMB-based concentration enhancement (ca. two to sixfold).

Characterization of the brewery spoilage bacterium Obesumbacterium proteus by automated ribotyping and development of PCR methods for its biotype 1

AIMS

To study the ability of automated ribotyping to characterize Obesumbacterium proteus and Hafnia alvei, to design primers and to evaluate standard end-point and real-time PCR for the detection of O. proteus biotype 1 in beer and in brewers's yeast-containing samples.

METHODS AND RESULTS

Automated ribotyping was carried out using the standard method with EcoRI and PvuII. The digestions with both enzymes clearly differentiated O. proteus biotypes 1 and 2 and H. alvei. PCR primers were designed according to the 16S rRNA gene sequence of the O. proteus type strain. Two primer sets (Obs137-Obs558 and Obs137-Obs617) detected O. proteus biotype 1 and H. alvei but not O. proteus biotype 2 or other tested beer spoilage bacteria (40 species) in the end-point and real-time PCR, indicating their high specificity. The detection limit for O. proteus was 160-1600 CFU 100 ml(-1) beer in the end-point PCR reactions and < or =160 CFU 100 ml(-1) beer in the real-time PCR reactions. More cells (from 16 to 3200) were needed for detection in the presence of brewer's yeast cells.

CONCLUSIONS

Automated ribotyping is a useful tool to characterize and identify O. proteus and H. alvei isolates. The designed primers are suitable for the rapid detection of O. proteus biotype 1 and H. alvei in brewery samples by PCR.

SIGNIFICANCE AND IMPACT OF THE STUDY

Automated ribotyping and PCR could improve microbiological quality control in breweries by facilitating the detection, identification and tracing of spoilage bacteria.

Rapid detection of Obesumbacterium proteus from yeast and wort using polymerase chain reaction

AIMS

To design and evaluate PCR primers for the rapid detection of Obesumbacterium proteus.

METHODS AND RESULTS

The 16S rDNA from a wild-type Obesumbacterium proteus biotype II isolate was sequenced and the resultant data used to produce specific primers for this organism. These primers discriminated between biotype I (nonbrewery) and biotype II isolates. In addition, the primers were able to detect Obesumbacterium proteus in wort and in yeast slurries in the presence of competitive bacteria. The primers were tested against a range of other beer spoilage bacteria for any cross-reactions. None were detected.

CONCLUSIONS

Obesumbacterium proteus primers can detect this contaminant without generating cross-reactions to related species.

SIGNIFICANCE AND IMPACT OF THE STUDY

The primers generated in this study can now be used for PCR detection assays that will contribute to early detection of this important process contaminant.