bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistence of Colonization of Human Colonic Mucosa by a Probiotic Strain,
Lactobacillus rhamnosus
GG, after Oral Consumption
Authors: Alander Minna , Satokari Reetta , Korpela Riitta , Saxelin Maija , Vilpponen-Salmela Terttu , Mattila-Sandholm Tiina , von Wright Atte 
Published: December 2019

ABSTRACT

Lactobacillus rhamnosus
GG is one of the most thoroughly studied probiotic strains. Its advantages in the treatment of gastrointestinal disorders are well documented. The aim of the present study was to demonstrate with colonic biopsies the attachment of strain GG to human intestinal mucosae and the persistence of the attachment after discontinuation of GG administration. A whey drink fermented with strain GG was fed to human volunteers for 12 days. Fecal samples were collected before, during, and after consumption.
L. rhamnosus
GG-like colonies were detected in both fecal and colonic biopsy samples. Strain GG was identified by its characteristic colony morphology, a lactose fermentation test, and PCR. This study showed that strain GG was able to attach in vivo to colonic mucosae and, although the attachment was temporary, to remain for more than a week after discontinuation of GG administration. The results demonstrate that the study of fecal samples alone is not sufficient in evaluating colonization by a probiotic strain.
Potential Role of
Thiobacillus caldus
in Arsenopyrite Bioleaching
Authors: Dopson Mark , Lindström E. Börje 
Published: December 2019

ABSTRACT

We investigated the potential role of the three strains of
Thiobacillus caldus
(KU, BC13, and C-SH12) in arsenopyrite leaching in combination with a moderately thermophilic iron oxidizer,
Sulfobacillus thermosulfidooxidans
. Pure cultures of
T. caldus
and
S. thermosulfidooxidans
were used as well as defined mixed cultures. By measuring released iron, tetrathionate, and sulfur concentrations, we found that the presence of
T. caldus
KU and BC13 in the defined mixed culture lowered the concentration of sulfur, and levels of tetrathionate were comparable to or lower than those in the presence of
S. thermosulfidooxidans
. This suggests that
T. caldus
grows on the sulfur compounds that build up during leaching, increasing the arsenopyrite-leaching efficiency. This result was similar to leaching arsenopyrite with a pure culture of
S. thermosulfidooxidans
in the presence of yeast extract. Therefore, three possible roles of
T. caldus
in the leaching environment can be hypothesized: to remove the buildup of solid sulfur that can cause an inhibitory layer on the surface of the mineral, to aid heterotrophic and mixotrophic growth by the release of organic chemicals, and to solubilize solid sulfur by the production of surface-active agents. The results showed that
T. caldus
KU was the most efficient at leaching arsenopyrite under the conditions tested, followed by BC13, and finally C-SH12.
Incidence of
Fusarium
spp. and Levels of Fumonisin B
1
in Maize in Western Kenya
Authors: Kedera C. J. , Plattner R. D. , Desjardins A. E. 
Published: December 2019

ABSTRACT

Maize kernel samples were collected in 1996 from smallholder farm storages in the districts of Bomet, Bungoma, Kakamega, Kericho, Kisii, Nandi, Siaya, Trans Nzoia, and Vihiga in the tropical highlands of western Kenya. Two-thirds of the samples were good-quality maize, and one-third were poor-quality maize with a high incidence of visibly diseased kernels. One hundred fifty-three maize samples were assessed for
Fusarium
infection by culturing kernels on a selective medium. The isolates obtained were identified to the species level based on morphology and on formation of the sexual stage in
Gibberella fujikuroi
mating population tests.
Fusarium moniliforme
(
G. fujikuroi
mating population A) was isolated most frequently, but
F. subglutinans
(
G. fujikuroi
mating population E),
F. graminearum
,
F. oxysporum
,
F. solani
, and other
Fusarium
species were also isolated. The high incidence of kernel infection with the fumonisin-producing species
F. moniliforme
indicated a potential for fumonisin contamination of Kenyan maize. However, analysis of 197 maize kernel samples by high-performance liquid chromatography found little fumonisin B
1
in most of the samples. Forty-seven percent of the samples contained fumonisin B
1
at levels above the detection limit (100 ng/g), but only 5% were above 1,000 ng/g, a proposed level of concern for human consumption. The four most-contaminated samples, with fumonisin B
1
levels ranging from 3,600 to 11,600 ng/g, were from poor-quality maize collected in the Kisii district. Many samples with a high incidence of visibly diseased kernels contained little or no fumonisin B
1
, despite the presence of
F. moniliforme
. This result may be attributable to the inability of
F. moniliforme
isolates present in Kenyan maize to produce fumonisins, to the presence of other ear rot fungi, and/or to environmental conditions unfavorable for fumonisin production.
Enumeration of Marine Viruses in Culture and Natural Samples by Flow Cytometry
Authors: Marie Dominique , Brussaard Corina P. D. , Thyrhaug Runar , Bratbak Gunnar , Vaulot Daniel 
Published: December 2019

ABSTRACT

Flow cytometry (FCM) was successfully used to enumerate viruses in seawater after staining with the nucleic acid-specific dye SYBR Green-I. The technique was first optimized by using the
Phaeocystis
lytic virus PpV-01. Then it was used to analyze natural samples from different oceanic locations. Virus samples were fixed with 0.5% glutaraldehyde and deep frozen for delayed analysis. The samples were then diluted in Tris-EDTA buffer and analyzed in the presence of SYBR Green-I. A duplicate sample was heated at 80°C in the presence of detergent before analysis. Virus counts obtained by FCM were highly correlated to, although slightly higher than, those obtained by epifluorescence microscopy or by transmission electron microscopy (
r
= 0.937,
n
= 14, and
r
= 0.96,
n
= 8, respectively). Analysis of a depth profile from the Mediterranean Sea revealed that the abundance of viruses displayed the same vertical trend as that of planktonic cells. FCM permits us to distinguish between at least two and sometimes three virus populations in natural samples. Because of its speed and accuracy, FCM should prove very useful for studies of virus infection in cultures and should allow us to better understand the structure and dynamics of virus populations in natural waters.
Use of the
KlADH4
Promoter for Ethanol-Dependent Production of Recombinant Human Serum Albumin in
Kluyveromyces lactis
Authors: Saliola Michele , Mazzoni Cristina , Solimando Nicola , Crisà Alessandra , Falcone Claudio , Jung Gerard , Fleer Reinhard 
Published: December 2019

ABSTRACT

KlADH4
is a gene of
Kluyveromyces lactis
encoding a mitochondrial alcohol dehydrogenase activity which is specifically induced by ethanol. The promoter of this gene was used for the expression of heterologous proteins in
K. lactis
, a very promising organism which can be used as an alternative host to
Saccharomyces cerevisiae
due to its good secretory properties. In this paper we report the ethanol-driven expression in
K. lactis
of the bacterial β-glucuronidase and of the human serum albumin (HSA) genes under the control of the
KlADH4
promoter. In particular, we studied the extracellular production of recombinant HSA (rHSA) with integrative and replicative vectors and obtained a significant increase in the amount of the protein with multicopy vectors, showing that no limitation of
KlADH4 trans
-acting factors occurred in the cells. By deletion analysis of the promoter, we identified an element (UAS
E
) which is sufficient for the induction of
KlADH4
by ethanol and, when inserted in the respective promoters, allows ethanol-dependent activation of other yeast genes, such as
PGK
and
LAC4
. We also analyzed the effect of medium composition on cell growth and protein secretion. A clear improvement in the production of the recombinant protein was achieved by shifting from batch cultures (0.3 g/liter) to fed-batch cultures (1 g/liter) with ethanol as the preferred carbon source.
Effects of Carbon Substrates on Nitrite Accumulation in Freshwater Sediments
Authors: Kelso Beverley H. L. , Smith Roger V. , Laughlin Ronald J. 
Published: December 2019

ABSTRACT

The contribution of the biochemical pathways nitrification, denitrification, and dissimilatory NO
3
−
reduction to NH
4
+
(DNRA) to the accumulation of NO
2
−
in freshwaters is governed by the species compositions of the bacterial populations resident in the sediments, available carbon (C) and nitrogen (N) substrates, and environmental conditions. Recent studies of major rivers in Northern Ireland have shown that high NO
2
−
concentrations found in summer, under warm, slow-flowing conditions, arise from anaerobic NO
3
−
reduction. Locally, agricultural pollutants entering rivers are important C and N sources, providing ideal substrates for the aquatic bacteria involved in cycling of N. In this study a range of organic C compounds commonly found in agricultural pollutants were provided as energy sources in 48-h incubation experiments to investigate if the chemical compositions of the pollutants affected which NO
3
−
reduction pathway was followed and influenced subsequent NO
2
−
accumulation. Carbon stored within the sediments was sufficient to support DNRA and denitrifier populations, and the resulting NO
2
−
peak (80 μg of N liter
−1
[approximate]) observed at 24 h was indicative of the simultaneous activities of both bacterial groups. The value of glycine as an energy source for denitrification or DNRA appeared to be limited, but glycine was an important source of additional N. Glucose was an efficient substrate for both the denitrification and DNRA pathways, with a NO
2
−
peak of 160 μg of N liter
−1
noted at 24 h. Addition of formate and acetate stimulated continuous NO
2
−
production throughout the 48-h period, caused by partial inhibition of the denitrification pathway. The formate treatment resulted in a high NO
2
−
accumulation (1,300 μg of N liter
−1
[approximate]), and acetate treatment resulted in a low NO
2
−
concentration (<100 μg of N liter
−1
).
A Method of Profiling Microbial Communities Based on a Most-Probable-Number Assay That Uses BIOLOG Plates and Multiple Sole Carbon Sources
Authors: Gamo Masashi , Shoji Tadashi 
Published: December 2019

ABSTRACT
A new approach to the community-level BIOLOG assay was proposed. This assay, which we call the BIOLOG-MPN assay, is a most-probable-number (MPN) assay that uses BIOLOG plates and multiple sole carbon sources, and the profiles obtained by this assay consist of MPNs estimated for the substrates in the BIOLOG plates. In order to demonstrate the performance of the BIOLOG-MPN assay, it was applied to pure cultures, model bacterial communities that contain two strains in different ratios, and microbial community samples. MPN estimation using BIOLOG plates worked well for the substrates on which utilizers can grow at a sufficiently high rate for color development under the conditions of the assay procedure. Furthermore, the results obtained using model communities showed that the MPNs obtained reflected the mixing ratios of pure cultures in the model communities. The profiles obtained using model communities and community samples were differentiated properly by statistical analyses. The results suggest that the BIOLOG-MPN assay is a promising procedure for obtaining a quantitative picture of the community structure.
Identification of
Enterococcus
spp. with a Biochemical Key
Authors: Manero Albert , Blanch Anicet R. 
Published: December 2019

ABSTRACT

A six-step biochemical key is presented for the identification of all recognized
Enterococcus
spp. The key consists of 12 tests, but no more than 6 are needed for the most complicated identification. The reliability of the key has been evaluated with collection type strains and clinical and environmental isolates. This key has fewer tests than those reported in previous studies. There is no commercial kit that includes the whole set of tests. However, some of the tests are included in enzyme activity-based kits that could be used with the proposed key. The key is designed for use in routine applications, especially in environmental and clinical studies with a high number of isolates.
Enhanced Production of Pediocin PA-1 and Coproduction of Nisin and Pediocin PA-1 by
Lactococcus lactis
Authors: Horn Nikki , Martínez María I. , Martínez José M. , Hernández Pablo E. , Gasson Michael J. , Rodríguez Juan M. , Dodd Helen M. 
Published: December 2019

ABSTRACT

The production and secretion of class II bacteriocins share a number of features that allow the interchange of genetic determinants between certain members of this group of antimicrobial peptides.
Lactococcus lactis
IL1403 encodes translocatory functions able to recognize and mediate secretion of lactococcin A. The ability of this strain to also produce the pediococcal bacteriocin pediocin PA-1, has been demonstrated previously by the introduction of a chimeric gene, composed of sequences encoding the leader of lactococcin A and the mature part of pediocin PA-1 (N. Horn, M. I. Martı́nez, J. M. Martı́nez, P. E. Hernández, M. J. Gasson, J. M. Rodrı́guez, and H. M. Dodd, Appl. Environ. Microbiol. 64:818–823, 1998). This heterologous expression system has been developed further with the introduction of the lactococcin A-dedicated translocatory function genes,
lcnC
and
lcnD
, and their effect on bacteriocin yields in various lactococcal hosts was assessed. The copy number of
lcnC
and
lcnD
influenced production levels, as did the particular strain employed as host. Highest yields were achieved with
L. lactis
IL1403, which generated pediocin PA-1 at a level similar to that for the parental strain,
Pediococcus acidilactici
347, representing a significant improvement over previous systems. The genetic determinants required for production of pediocin PA-1 were introduced into the nisin-producing strain
L. lactis
FI5876, where both pediocin PA-1 and nisin A were simultaneously produced. The implications of coproduction of these two industrially relevant antimicrobial agents by a food-grade organism are discussed.
Enhanced Biotransformation of Carbon Tetrachloride by
Acetobacterium woodii
upon Addition of Hydroxocobalamin and Fructose
Authors: Hashsham Syed A. , Freedman David L. 
Published: December 2019

ABSTRACT

The objective of this study was to evaluate the effect of hydroxocobalamin (OH-Cbl) on transformation of high concentrations of carbon tetrachloride (CT) by
Acetobacterium woodii
(ATCC 29683). Complete transformation of 470 μM (72 mg/liter [aqueous]) CT was achieved by
A. woodii
within 2.5 days, when 10 μM OH-Cbl was added along with 25.2 mM fructose. This was approximately 30 times faster than
A. woodii
cultures (live or autoclaved) and medium that did not receive OH-Cbl and 5 times faster than those controls that did receive OH-Cbl, but either live
A. woodii
or fructose was missing. CT transformation in treatments with only OH-Cbl was indicative of the important contribution of nonenzymatic reactions. Besides increasing the rate of CT transformation, addition of fructose and OH-Cbl to live cultures increased the percentage of [
14
C]CT transformed to
14
CO
2
(up to 31%) and
14
C-labeled soluble materials (principally
l
-lactate and acetate), while decreasing the percentage of CT reduced to chloroform and abiotically transformed to carbon disulfide.
14
CS
2
represented more than 35% of the [
14
C]CT in the presence of reduced medium and OH-Cbl. Conversion of CT to CO was a predominant pathway in formation of CO
2
in the presence of live cells and added fructose and OH-Cbl. These results indicate that the rate and distribution of products during cometabolic transformation of CT by
A. woodii
can be improved by the addition of fructose and OH-Cbl.
Effect of Milk Proteins on Adhesion of Bacteria to Stainless Steel Surfaces
Authors: Barnes L.-M. , Lo M. F. , Adams M. R. , Chamberlain A. H. L. 
Published: December 2019

ABSTRACT

Stainless steel coupons were treated with skim milk and subsequently challenged with individual bacterial suspensions of
Staphylococcus aureus
,
Pseudomonas fragi
,
Escherichia coli
,
Listeria monocytogenes
, and
Serratia marcescens
. The numbers of attached bacteria were determined by direct epifluorescence microscopy and compared with the attachment levels on clean stainless steel with two different surface finishes. Skim milk was found to reduce adhesion of
S. aureus
,
L. monocytogenes
, and
S. marcescens
.
P. fragi
and
E. coli
attached in very small numbers to the clear surfaces, making the effect of any adsorbed protein layer difficult to assess. Individual milk proteins α-casein, β-casein, κ-casein, and α-lactalbumin were also found to reduce the adhesion of
S. aureus
and
L. monocytogenes
. The adhesion of bacteria to samples treated with milk dilutions up to 0.001% was investigated. X-ray photoelectron spectroscopy was used to determine the proportion of nitrogen in the adsorbed films. Attached bacterial numbers were inversely related to the relative atomic percentage of nitrogen on the surface. A comparison of two types of stainless steel surface, a 2B and a no. 8 mirror finish, indicated that the difference in these levels of surface roughness did not greatly affect bacterial attachment, and reduction in adhesion to a milk-treated surface was still observed. Cross-linking of adsorbed proteins partially reversed the inhibition of bacterial attachment, indicating that protein chain mobility and steric exclusion may be important in this phenomenon.
Automated Approach for Ribosomal Intergenic Spacer Analysis of Microbial Diversity and Its Application to Freshwater Bacterial Communities
Authors: Fisher Madeline M. , Triplett Eric W. 
Published: December 2019

ABSTRACT
An automated method of ribosomal intergenic spacer analysis (ARISA) was developed for the rapid estimation of microbial diversity and community composition in freshwater environments. Following isolation of total community DNA, PCR amplification of the 16S-23S intergenic spacer region in the rRNA operon was performed with a fluorescence-labeled forward primer. ARISA-PCR fragments ranging in size from 400 to 1,200 bp were next discriminated and measured by using an automated electrophoresis system. Database information on the 16S-23S intergenic spacer was also examined, to understand the potential biases in diversity estimates provided by ARISA. In the analysis of three natural freshwater bacterial communities, ARISA was rapid and sensitive and provided highly reproducible community-specific profiles at all levels of replication tested. The ARISA profiles of the freshwater communities were quantitatively compared in terms of both their relative diversity and similarity level. The three communities had distinctly different profiles but were similar in their total number of fragments (range, 34 to 41). In addition, the pattern of major amplification products in representative profiles was not significantly altered when the PCR cycle number was reduced from 30 to 15, but the number of minor products (near the limit of detection) was sensitive to changes in cycling parameters. Overall, the results suggest that ARISA is a rapid and effective community analysis technique that can be used in conjunction with more accurate but labor-intensive methods (e.g., 16S rRNA gene cloning and sequencing) when fine-scale spatial and temporal resolution is needed.
A Method To Detect Low Levels of Enteric Viruses in Contaminated Oysters
Authors: Shieh Y.-S. Carol , Calci Kevin R. , Baric Ralph S. 
Published: December 2019

ABSTRACT
Direct isolation and identification of pathogenic viruses from oysters implicated in gastroenteritis outbreaks are hampered by inefficient methods for recovering viruses, naturally occurring PCR inhibitors, and low levels of virus contamination. In this study we focused on developing rapid and efficient oyster-processing procedures that can be used for sensitive PCR detection of viruses in raw oysters. Poliovirus type 3 (PV3) Sabin strain was used to evaluate the efficacy of virus recovery and the removal of PCR inhibitors during oyster-processing procedures. These procedures included elution, polyethylene glycol precipitation, solvent extraction, and RNA extraction. Acid adsorption-elution in which glycine buffer (pH 7.5) was used was found to retain fewer inhibitors than direct elution in which glycine buffer (pH 9.5) was used. RNA extraction in which a silica gel membrane was used was more effective than single-step RNA precipitation for removing additional nonspecific PCR inhibitors. The final 10-μl volume of RNA concentrates obtained from 2 g of oyster tissue (concentration factor, 200-fold) was satisfactory for efficient reverse transcription-PCR detection of virus. The overall detection sensitivity of our method was 1 PFU/g of oyster tissue initially seeded with PV3. The method was utilized to investigate a 1998 gastroenteritis outbreak in California in which contaminated oysters were the suspected disease transmission vehicle. A genogroup II Norwalk-like virus was found in two of three recalled oyster samples linked by tags to the harvest dates and areas associated with the majority of cases. The method described here improves the response to outbreaks and can be used for rapid and sensitive detection of viral agents in outbreak-implicated oysters.
Quantification of Syntrophic Fatty Acid-β-Oxidizing Bacteria in a Mesophilic Biogas Reactor by Oligonucleotide Probe Hybridization
Authors: Hansen Kaare H. , Ahring Birgitte K. , Raskin Lutgarde 
Published: December 2019

ABSTRACT

Small-subunit rRNA sequences were obtained for two saturated fatty acid-β-oxidizing syntrophic bacteria,
Syntrophomonas sapovorans
and
Syntrophomonas wolfei
LYB, and sequence analysis confirmed their classification as members of the family
Syntrophomonadaceae
.
S. wolfei
LYB was closely related to
S. wolfei
subsp.
wolfei
, but
S. sapovorans
did not cluster with the other members of the genus
Syntrophomonas
. Five oligonucleotide probes targeting the small-subunit rRNA of different groups within the family
Syntrophomonadaceae
, which contains all currently known saturated fatty acid-β-oxidizing syntrophic bacteria, were developed and characterized. The probes were designed to be specific at the family, genus, and species levels and were characterized by temperature-of-dissociation and specificity studies. To demonstrate the usefulness of the probes for the detection and quantification of saturated fatty acid-β-oxidizing syntrophic bacteria in methanogenic environments, the microbial community structure of a sample from a full-scale biogas plant was determined. Hybridization results with probes for syntrophic bacteria and methanogens were compared to specific methanogenic activities and microbial numbers determined with most-probable-number estimates. Most of the methanogenic rRNA was comprised of
Methanomicrobiales
rRNA, suggesting that members of this order served as the main hydrogen-utilizing microorganisms. Between 0.2 and 1% of the rRNA was attributed to the
Syntrophomonadaceae
, of which the majority was accounted for by the genus
Syntrophomonas
.