Predominant Bacterial Populations Research Articles

Bacterial community associated to histamine contamination in sardines: a case study in the canned fish industry

This study aimed to identify the predominant bacterial populations in sardine samples with high histamine content (≥ 200 mg*kg-1) and histamine-free (< 1 mg*kg-1). For this study, 1,000 g of muscle samples were collected from 40–45 sardines per batch, all obtained from the same supplier, fishing area and period, for histamine analysis. Samples (1 g) from five different batches with ≥ 200 mg*kg-1 of histamine (named histamine group) and five with < 1 mg*kg-1 (named no-histamine group) were submitted to microbial analysis by extracting the total DNA, followed by polymerase chain reaction of the V3-V4 region of 16S rRNA gene and Ilumina sequencing (Mi-Seq, paired-end). In total, 18 different operational taxonomic units were identified in all samples. Sardines with high histamine content exhibited lower microbial diversity and a higher abundance of the genera Photobacterium and Shewanella. These bacteria thrive under mild temperatures and indicate fish spoilage and the production of biogenic amines. In contrast, Psychrobacter and Pseudoalteromonas, known to withstand harsh conditions, including low temperatures, were more prevalent in histamine-free sardines. Our findings point out to a marked change in the bacterial community of sardines with high and no histamine content, even though they are from the same fishing area, period, and shipment.

Enhancing biomethanation performance through co-digestion of diverse organic wastes: a comprehensive study on substrate optimization, inoculum selection, and microbial community analysis.

A blend of organic municipal solid waste, slaughterhouse waste, fecal sludge, and landfill leachate was selected in different mixing ratios to formulate the best substrate mixture for biomethanation. Individual substrates were characterized, and the mixing ratio was optimized with the help of a response surface methodology tool to a value of 1:1:1:1 (with a C/N ratio of 28±0.769 and total volatile fatty acid (VFA) concentration of 2500±10.53 mg/L) to improve the overall biomethanation. The optimized blend (C/N ratio: 28.6, VFA: 2538 mg/L) was characterized for physicochemical, biological, and microbial properties and subjected to anaerobic digestion in lab-scale reactors of 1000 mL capacity with and without the addition of inoculum. The biogas yield of individual substrates and blends was ascertained separately. The observed cumulative biogas yield over 21 days from the non-inoculated substrates varied between 142±1.95 mL (24.6±0.3 ml/gVS) and 1974.5±21.72 mL (270.4±3.1 ml/gVS). In comparison, the addition of external inoculation at a 5% rate (w/w) of the substrate uplifted the minimum and maximum cumulative gas yield values to 203±9.9 mL (35.0±1.6 mL/gVS) and 3394±13.4 mL (315.3±1.2 mL/gVS), respectively. The inoculum procured from the Defence Research and Development Organisation (DRDO) was screened in advance, considering factors such as maximizing VFA production and consumption rate, biogas yield, and digestate quality. A similar outcome regarding biogas yield and digestate quality was observed for the equivalent blend. The cumulative gas yield increased from 2673±14.5 mL (373.7±2.2 mL/gVS) to 4284±111.02 mL (391.47±20.02 mL/gVS) over 21 days post-application of a similar dosage of DRDO inoculum. The 16S rRNA genomic analysis revealed that the predominant bacterial population belonged to the phylum Firmicutes, with the majority falling within the orders Clostridiales and Lactobacillales. Ultimately, the study advocates the potential of the blend mentioned above for biomethanation and concomitant enrichment of both biogas yield and digestate quality.

Buffalo feed efficiency: optimizing the use of fibrous biomass carbon to enhance production while mitigating rumen methane emission

Buffaloes are one of the important ruminants contributing to food security in the form of meat and milk, as well as their by-products such as skin, horns, and manure. The buffalo’s meat, milk, and their products have been revealed to have high nutritious values, especially the protein and amino acids profiles and some essential bioactive compounds for health and well-being. Above all, the buffaloes are the smart ruminants in converting the high fibrous feeds, in particular, the agricultural biomass and industrial by-products, by enhancing the rumen fermentation end-products via the anaerobic Embden-Mey-erhof-Parnas pathway while mitigating rumen methane emission. Concerning the rumen microbiomes of buffaloes, it has been reported that they were highly diversified and relatively higher-abundant compared to cattle, leading to enhanced total volatile fatty acids (VFAs) and lower methane production, the biogenic methane. The current advanced analysis using Next-Generation Sequencing (NGS) of rumen microbiomes offered a more insightful understanding of their ability to degrade more fibrous feeds, especially agricultural crop residues, low-quality roughages, and some plastic materials. Relative abundances of the predominant bacterial population have been found under the phyla; Firmicutes and Bacteroidetes such as Ruminococcus albus, Ruminococcus flavefeciens, and Fibro-bacter succinogenes and Prevotella ruminocola. Enormous agricultural biomass has been commonly available globally as a result of crop cultivation, especially those of straws, stovers, vines, and tops, as well as industrial by-products such as pineapple peels, cassava pulp, sugarcane bagasse, sorghum residues. Despite their abundance, their nutritive values contain a low crude protein level, and high lignocellulosic is additionally encountered. Hence, simple and practical pre-treatment such as the urea-lime (2+2% U-lime) has been successfully exploited to enhance the crude protein content and digestibility of nutrients while mitigating the rumen methane production. The U-lime treated rice straw and supplementation of phyto-nutrient fruit-peel pellets (MARABAC) have significantly improved rumen fermentation in the ruminants. Therefore, dietary manipulation based on the pre-treatment of the fibrous feeds and supplementation of phytonutrient pellets should be more intervened. Furthermore, the feeding interventions based on the use of locally available resources should be extensively exploited, focusing on the hands-on establishment (E), development (D), utilization (U), and sustainability (S) (EDUS) for all engaged stakeholders of farm level up to the industrial plat- form, ultimately, the buffalo production scenario would be economically viable and environmentally friendly system.

Semi-continuous anaerobic co-digestion of thermal and thermal-alkali processed organic fraction of municipal solid waste: Methane yield, energy analysis, anaerobic microbiome

The semi-continuous anaerobic co-digestion (AcoD) of thermal and thermal-alkali pretreated organic fraction of municipal solid waste (OFMSW) and sewage sludge (SS) was studied under varying hydraulic retention times (HRT) and organic loading rates (OLR Three semi-continuous digesters were operated under control (non-pre-treated), thermally pretreated (125 °C), and thermal-alkali pretreated (125°C-3g/L NaOH) conditions at variable OLRs at 2.5, 4.0, 5.1, and 7.6 kgVS/m3.d and corresponding HRTs of 30, 20, 15, and 10 days. The 10 and 43% higher methane yield (0.445 m3/kgVS) and 11 and 57% higher VS removal (52%) was achieved for thermal-alkali pretreated digester at 5.1 kgVS/m3.d OLR over thermally pretreated (0.408 m3/kgVS, 45% VS removal) and control digesters (0.310 m3/kgVS, 33% VS removal), respectively. Thermal and thermal-alkali digesters failed on increasing the OLR to 7.6 kgVS/m3.d, whereas the control digester becomes upset at 5.1 kgVS/m3.d OLR. The metagenomic study revealed that Firmicutes, Bacteroidetes, Chloroflexi, Euryarchaeota, Proteobacteria, and Actinobacteria were the predominant bacterial population, whereas Methanosarcina and Methanothrix dominated the archaeal community. Energy balance analysis revealed that thermal alkali pretreatment showed the highest positive energy balance of 114.6 MJ/ton with an energy ratio of 1.25 compared with thermally pretreated (81.5 MJ/ton) and control samples (−46.9 MJ/ton). This work pave the way for scaleup of both thermal and thermal-alkali pre-treatment at 125 °C to realize the techno-economic and energy potential of the process.

Reaction of <i>Bifidobacterium longum</i> subsp. <i>infantis</i> Strain ATCC 15697 to Oxidative Stress

The genus Bifidobacterium is one of the predominant bacterial populations in human gut microbiota. Despite the increasing number of studies on the beneficial functionality of bifidobacteria for human health, knowledge about their antioxidant potential is still insufficient. The role of the antioxidant potential of bifidobacteria in maintaining the homeostasis of the intestinal microbiota of the host organism as a whole is an important task that requires solutions. For the first time, this paper presents the data of genomic, transcriptomic and proteomic analyses of probiotic strains Bifidobacterium longum subsp. infantis ATCC 15697 after the action of oxidative stress. The growing culture of strain was exposed to hydrogen peroxide for 2 hours and oxygen for 2 and 4 hours. Preliminary genome analysis of the strain showed the presence of 18 genes encoding a known protein with antioxidant function, as in other complied genomes of B. longum subsp. infantis strains available in the international database. The complete transcriptome analysis revealed an increase in transcript levels by more than two times for 6 genes with a known antioxidant function. The data of quantitative proteomic analysis showed an increase in protein levels by more than two times for five enzymes with a known antioxidant function. 28 other proteins with increased levels more than twice were identified in the cells of the growing culture in response to the long action of oxygen. These proteins can be involved in the processes of the cell’s response to stress, the amino acids, nucleotides metabolism and transport processes. Six proteins with unknown functions, which may play a significant role in the antioxidant response of anaerobic bifidobacteria, were found to have high levels in the cells after the action of stress. The obtained data are supposed to be used in the selection of B. longum subsp. infantis strains and the creation of pharmacobiotics able to correct the composition of the microbiota.

Assessment of Microbial Diversity during Thermophilic Anaerobic Co-Digestion for an Effective Valorization of Food Waste and Wheat Straw

In this study, predominant bacterial and archaeal populations and their roles during anaerobic mono-digestion of food waste (FW) and co-digestion of FW with straw pellets (SP) at thermophilic temperature (53 ± 1 °C) were assessed by Next Generation Sequencing (NGS) analysis at organic loading rates (OLRs) of 3.0 and 7.0 gVS/L/d. Depending on the seed; results revealed that Firmicutes, Bacteroidetes, and Proteobacteria were, respectively the most prevalent bacterial phyla at both OLRs investigated. On the other hand, Euryarchaeota was dominated by methanogens playing crucial role in biogas production and correlated mainly with the activities of Methanobacteria and Methanomicrobia at class level. Acetoclastic Methanosaetae was the predominant genus at OLR = 3.0 gVS/L/d; however, shared the same predominance with hydrogenotrophic methanogens Methanospirillium at the highest OLR. Although no clear effect in response to straw addition at OLR of 3.0 gVS/L/d could be seen in terms of methanogenic archaea at genus level, hydrogenotrophic methanogens revealed some shift from Methanobacterium to Methanospirillium at higher OLR. Nevertheless, no prominent microbial shift in the presence of wheat straw at increased OLR was likely due to adapted inoculation at start-up which was also demonstrated by relatively stable biogas yields during co-digestion.

A preliminary study of the effect of total fishmeal replacement with different dietary sources on the gut microbiota of spotted rose snapper juvenile ( Lutjanus guttatus Steindachner, 1869)

The aims of this preliminary study were (a) to evaluate the effect of replacing total fishmeal (FM) protein (crude protein, 70.7% CP) with terrestrial animal by-products (porcine meat and poultry by-products; 59.7% CP and 61.6% respectively) and plant meal (soya bean concentrate and corn gluten; CP = 47.3% and 72.7% respectively) on the gut microbiota of Lutjanus guttatus juveniles and (b) to assess the effect of intermittent feeding in transient microbiota. Organisms (106 ± 12 g) were fed a FM, terrestrial animal by-products (PPM) or plant (VEGM)-based diet for ten days; afterwards, they were fed FM diet for ten more days. Samples were analysed using 16S rRNA taxonomic fingerprinting, and function profile analysis was determined by PICRUSt. Serratia and Burkholderia were representative of resident microbiota, while Photobacterium and Vibrio were the predominant genera in transient microbiota. Nor the total FM replacement by PPM and VEGM, nor the intermittent feeding, affected the predominant bacterial populations in the snapper gut microbiota, but significant changes in the amino acid metabolism pathway were observed in PPM group. This research might provide a guideline to define alternative ingredients to fishmeal in order to develop more sustainable diets without negatively affecting the intestinal microbiota composition.

Assessment of predominant bacteria in noble pen shell (Pinna nobilis) collected in the Eastern Adriatic Sea.

Noble pen shell (Pinna nobilis) is an endemic species and the largest known bivalve in the Mediterranean Sea. By filtering large amounts of water, they maintain a high percentage of organic matter, hence playing an important role in the marine ecosystem. The ecological community of pen shells is impressive, and there are numerous microorganisms present in its soft tissues. Since this species is highly endangered due to recently described mass mortalities throughout the Mediterranean, this study was aimed at finding out more about its microbiome. In this study, we identified the predominant bacterial populations of specimens collected at three separate locations along the Eastern Adriatic coast. The predominant bacteria were isolated and 16S rRNA sequencing was performed to identify eight different bacterial genera: Aestuariibacter sp., Aliivibrio sp., Alteromonas sp., Marinobacter sp., Pseudoalteromonas sp., Rubritalea sp., Thalassospira sp. and the Vibrio splendidus clade. The identified genera are ubiquitous in the marine environment and have previously been described as both beneficial symbionts and potential pathogens in other molluscs. There was a clear difference in the predominant bacterial populations between northern and southern sampling sites, which could be linked to water temperature. These findings indicate the need for expanded sampling over a longer time period, since more exhaustive research would provide information vital to the conservation of this critically endangered species.

Wheat Bran Cereal, Human Gut Bacteria and Subjective Wellbeing

Research has shown that consumption of high fiber breakfast cereal is associated with improved subjective well-being, especially increased energy. One possible explanation of these results is through metabolism by gut bacteria and concomitant production of metabolites that influence psychological and gastrointestinal (GI) welfare. This was examined in the present study to determine whether consumption of wheat bran could modulate the composition of the GI microbiota. This human volunteer study (20 volunteers) involved the comparison of three breakfast cereals, All-Bran, Bran Flakes and Cornflakes (60 g/d). The study involved a 14-day baseline phase (no breakfast cereals) and an eight-week experimental phase. Each cereal was consumed for 14 days. A seven-day washout period (no cereals) was carried out between each successive cereal condition. Faecal samples were collected every seven days. Enumeration of predominant faecal bacterial populations (bacteroides, bifidobacteria, clostridia, lactobacilli and eubacteria) was carried out using the culture independent fluorescent in situ hybridisation (FISH) technique. Faecal short chain fatty acid content was also determined. The volunteers completed a battery of questionnaires to assess fatigue/energy, subjective mood, physical and mental health, bowel function and fiber intake. The results showed that in general there was no overall significant effect of breakfast cereal type on the faecal bacterial populations studied. There was also no major effect of breakfast type on short chain fatty acid content. The high-fiber conditions (All-Bran and Bran Flakes) were associated with less fatigue, a significant reduction in cognitive difficulties, looser stools, more motions and feeling more energised.

Dynamic changes of bacterial community in activated sludge with pressurized aeration in a sequencing batch reactor.

This study aimed to investigate the organic removal efficiency and microbial population dynamics in activated sludge with pressurized aeration. The activated sludge was fed with synthetic wastewater composed of simple carbon source to avoid the effect of complex components on microbial communities. The pressurized acclimation process was conducted in a bench-scale sequencing batch reactor (SBR) under 0.3 MPa gage pressure. Another SBR was running in atmospheric environment as a control reactor, with the same operation parameters except for the pressure. Bacterial diversity was investigated by Illumina sequencing technology. The results showed that the total organic carbon removal efficiency of the pressurized reactor was significantly higher, while the mixed liquor suspended solids concentrations were much lower than those of the control reactor. Moderate pressure of 0.3 MPa had little effect on Alpha-diversity of bacterial communities due to the similar running conditions, e.g., feed water, solids retention time (SRT) and the cyclic change of dissolved oxygen (DO) concentrations. Although the relative percentage of the bacterial community changed among samples, there was no major change of predominant bacterial populations between the pressurized group and the control group. Pressurized aeration would have a far-reaching impact on microbial community in activated sludge when treating wastewaters being unfavorable to the dissolution of oxygen.

Enzymatic C[sbnd]C bond formation by benzylsuccinate synthases – A key step in anaerobic microbial degradation of hydrocarbons

In cases where fire debris contains soil, microorganisms can rapidly and irreversibly alter the chemical composition of any ignitable liquid residue that may be present. In this study, differences in microbial degradation due to the season in which the sample is collected was examined. Soil samples were collected from the same site during Fall, Winter, Spring and Summer and the degradation of gasoline was monitored over 30 days. Predominant viable bacterial populations enumerated using real-time PCR and reverse transcriptase polymerase chain reaction (RT-PCR) enumeration revealed the predominant viable bacterial genera to be Alcaligenes, Bacillus, and Flavobacterium. Overall, the compounds most vulnerable to microbial degradation are the n-alkanes, followed by the mono-substituted alkylbenzenes (e.g., toluene, ethylbenzene, propylbenzene and isopropylbenzene). Benzaldehyde (a degradation product of toluene) was also identified as a marker for the extent of biodegradation. Ultimately, it was determined that soil collected during an unusually hot and dry summer exhibited the least degradation with little to no change in gasoline for up to 4 days, readily detectable n-alkanes for up to 7 days and relatively high levels of resilient compounds such as o-xylene, p-xylene and 1,3,5-trimethylbenzene. These results demonstrate, however, that prompt preservation and/or analysis of soil evidence is required in order to properly classify an ignitable liquid residue.

Improving rumen ecology and microbial population by dried rumen digesta in beef cattle.

Four Thai native beef cattle with initial body weight (BW) of 91.8 ± 4.75kg were randomly assigned according to a 4 × 4 Latin square design to receive four concentrates replacement levels of soybean meal (SBM) by dried rumen digesta (DRD) at 0, 33, 67, and 100% on dry matter (DM) basis. All cattle were fed rice straw ad libitum while additional concentrate was fed at 0.5% BW daily. The experiment was conducted for four periods of 21days. Rumen fluid was analyzed for predominant cellulolytic bacterial population by using real-time PCR technique. Increasing levels of DRD did not alter total feed intake, ruminal pH and temperature, and plasma urea nitrogen (P > 0.05). Protozoa and fungal population were not differed by DRD supplementation while population of bacteria at 4h post feeding was increased when SBM was replaced with DRD at 66 and 100% DM. Population of total bacteria and R. flavefaciens at 4h post feeding were significantly highest with inclusion of 100% of DRD in the ration. The experimental diets has no effect on excretion and absorption of purine derivatives (P > 0.05), while microbial crude protein and efficiency of microbial N synthesis were significantly increased with DRD inclusion in the diet and highest with 100% DRD replacement (P > 0.05). Replacement of SBM by DRD at 100% DM improved the rumen ecology and microbial population in beef cattle fed on rice straw.

Microbial degradation of gasoline in soil: Effect of season of sampling

In cases where fire debris contains soil, microorganisms can rapidly and irreversibly alter the chemical composition of any ignitable liquid residue that may be present. In this study, differences in microbial degradation due to the season in which the sample is collected was examined. Soil samples were collected from the same site during Fall, Winter, Spring and Summer and the degradation of gasoline was monitored over 30 days. Predominant viable bacterial populations enumerated using real-time PCR and reverse transcriptase polymerase chain reaction (RT-PCR) enumeration revealed the predominant viable bacterial genera to be Alcaligenes, Bacillus, and Flavobacterium. Overall, the compounds most vulnerable to microbial degradation are the n-alkanes, followed by the mono-substituted alkylbenzenes (e.g., toluene, ethylbenzene, propylbenzene and isopropylbenzene). Benzaldehyde (a degradation product of toluene) was also identified as a marker for the extent of biodegradation. Ultimately, it was determined that soil collected during an unusually hot and dry summer exhibited the least degradation with little to no change in gasoline for up to 4 days, readily detectable n-alkanes for up to 7 days and relatively high levels of resilient compounds such as o-xylene, p-xylene and 1,3,5-trimethylbenzene. These results demonstrate, however, that prompt preservation and/or analysis of soil evidence is required in order to properly classify an ignitable liquid residue.

Microbial Degradation of Gasoline in Soil: Comparison by Soil Type

During the investigation of a suspicious fire, debris is often collected from the scene and analyzed for residues of ignitable liquids (e.g., gasoline). In cases where the debris is contaminated with soil, it is known that heterotrophic soil microorganisms can alter the chemical composition of the ignitable liquid residue over time. The effects of soil type and season upon this phenomenon are not known, however. Hence, soil collected from locations under three different uses (residential, agricultural, brownfield) were spiked with gasoline and microbial degradation was monitored for 30 days. The soils were also chemically and biologically characterized. Gas chromatographic profiles showed that residential soil was most active and brownfield soil least active for the microbial degradation of gasoline. The brownfield soil possessed relatively high (497 mg/kg) concentrations of Pb, which may have affected bacterial activity. Predominant viable bacterial populations enumerated using real-time reverse transcriptase polymerase chain reaction (RT-PCR) included members of the Alcaligenes, Acinetobacter, Arthrobacter, Bacillus, Flavobacterium, and Pseudomonas genera. Principal Components Analysis (PCA) was found effective in elucidating trends of microbial degradation among the different soil types and seasons. The results of this study demonstrate the necessity of prompt analysis of forensic evidence for proper identification of possible ignitable liquids.

Physiological characteristics of predominant ammonia-oxidizing bacteria enriched from bioreactors with different influent supply regimes

Two acclimatized biomasses exposed to ammonium (NH4+) concentration of 600mg NL−1, one from a completely stirred tank reactor (CSTR), the other from a sequencing batch reactor (SBR), were assayed for nitritation performance, predominant nitrifying bacterial population and nitrous oxide (N2O) production. By virtue of fluctuating and constant NH4+ concentrations respectively, the SBR and CSTR wastewater supply regimes were hypothesized to support different predominant ammonia-oxidizing bacteria (AOB) exhibiting distinct biokinetic properties. Nitritation efficiency (NO2−-N/NO2+3−-N) was higher in the SBR (89%) than the CSTR (30%) likely due to free ammonia and dissolved oxygen concentration. Quantitative fluorescence in situ hybridization (FISH) analyses revealed that fast-growing (r-strategist) AOB of halophilic and halotolerant Nitrosomonas lineage were more highly enriched in the SBR (76±4.2%) than the CSTR (38±6.0%). The CSTR predominantly enriched slow-growing (K-strategist) AOB Nitrosospira spp. (42±1.9% versus 1.4±0.8% in the SBR). Biokinetic parameter estimation consolidated the FISH result: the maximum growth rate and half-saturation coefficients for NH4+ were higher in the SBR (μmax=0.92 day, KNH4+=28.9mg NL−1) relative to the CSTR (μmax=0.42 day, KNH4+=3.47mg NL−1), suggesting that the extent of nitritation may be controlled by choice of wastewater influent operational regime, which itself determines predominant AOB. N2O production was a maximum of 25 times higher (10.2mg N-N2Oh−1 at 0.5mg O2L−1) in CSTR-enriched biomass than in SBR-enriched biomass (0.41mg N-N2Oh−1 at 0.5mg O2L−1).

Microbial composition during Chinese soy sauce koji-making based on culture dependent and independent methods

Koji-making is a key process for production of high quality soy sauce. The microbial composition during koji-making was investigated by culture-dependent and culture-independent methods to determine predominant bacterial and fungal populations. The culture-dependent methods used were direct culture and colony morphology observation, and PCR amplification of 16S/26S rDNA fragments followed by sequencing analysis. The culture-independent method was based on the analysis of 16S/26S rDNA clone libraries. There were differences between the results obtained by different methods. However, sufficient overlap existed between the different methods to identify potentially significant microbial groups. 16 and 20 different bacterial species were identified using culture-dependent and culture-independent methods, respectively. 7 species could be identified by both methods. The most predominant bacterial genera were Weissella and Staphylococcus. Both 6 different fungal species were identified using culture-dependent and culture-independent methods, respectively. Only 3 species could be identified by both sets of methods. The most predominant fungi were Aspergillus and Candida species. This work illustrated the importance of a comprehensive polyphasic approach in the analysis of microbial composition during soy sauce koji-making, the knowledge of which will enable further optimization of microbial composition and quality control of koji to upgrade Chinese traditional soy sauce product.

Changes in microbial community structure in two anaerobic systems to treat bagasse spraying wastewater with and without addition of molasses alcohol wastewater

This study investigates the microbial community and structure in the internal circulation (IC) reactors that treat wastewater from bagasse spraying, with (reactor B) and without (reactor A) addition of molasses alcohol wastewater (MAW). The V3 regions in the 16S rRNA of bacteria were sequenced using illumina sequencing to characterize the microbial community structures. The results showed that there were approximately 34.8% more microorganisms were reduced, while the proportions of the three most predominant bacterial populations especially some sulfate-reducing bacteria increased in reactor B. The archaeal community composition was measured by PCR-DGGE (denaturing gradient gel electrophoresis) analysis and sequencing some clones from the 16S rRNA gene library. The results showed that numerous, mostly uncharacterized, archaeal genera are present in reactors A and B; the genus Methanomethylovorans was only detected in the samples that received MAW. This study demonstrated the significant effect of MAW on microbial communities in the wastewater treatment bioreactor.

Acquired Antibiotic Resistance: Are We Born with It?

The rapid emergence of antibiotic resistance (AR) is a major public health concern. Recent findings on the prevalence of food-borne antibiotic-resistant (ART) commensal bacteria in ready-to-consume food products suggested that daily food consumption likely serves as a major avenue for dissemination of ART bacteria from the food chain to human hosts. To properly assess the impact of various factors, including the food chain, on AR development in hosts, it is important to determine the baseline of ART bacteria in the human gastrointestinal (GI) tract. We thus examined the gut microbiota of 16 infant subjects, from the newborn stage to 1 year of age, who fed on breast milk and/or infant formula during the early stages of development and had no prior exposure to antibiotics. Predominant bacterial populations resistant to several antibiotics and multiple resistance genes were found in the infant GI tracts within the first week of age. Several ART population transitions were also observed in the absence of antibiotic exposure and dietary changes. Representative AR gene pools including tet(M), ermB, sul2, and bla(TEM) were detected in infant subjects. Enterococcus spp., Staphylococcus spp., Klebsiella spp., Streptococcus spp., and Escherichia coli/Shigella spp. were among the identified AR gene carriers. ART bacteria were not detected in the infant formula and infant foods examined, but small numbers of skin-associated ART bacteria were found in certain breast milk samples. The data suggest that the early development of AR in the human gut microbiota is independent of infants' exposure to antibiotics but is likely impacted by exposure to maternal and environmental microbes during and after delivery and that the ART population is significantly amplified within the host even in the absence of antibiotic selective pressure.

The intestinal microbial diversity in Chinese shrimp ( Fenneropenaeus chinensis) as determined by PCR–DGGE and clone library analyses

In this study, the intestinal microbiota of Chinese shrimp ( Fenneropenaeus chinensis) was examined by molecular analysis of the 16S rDNA. The aims of the study were to evaluate the use of molecular-based techniques, Polymerase Chain Reaction/Denaturing Gradient Gel Electrophoresis (PCR–DGGE) and clone library analyses, and compare the results obtained by the two methods. Total DNA was extracted from the intestine of Chinese shrimp. Then population fingerprints of the predominant microbiota were generated by DGGE analysis of universal V3 16S rDNA PCR amplicons, and 22 distinct bands from DGGE were sequenced. In addition, bacterial 16S rRNA gene was amplified with universal bacterial primers 27F and 1387R. Amplicons were ligated into cloning vectors and near-full-length 16S rRNA gene inserts were analyzed. A clone library was constructed and 72 clones were sequenced. The results suggested that PCR–DGGE and clone library analysis were effective techniques for monitoring and analyzing the intestinal microbial diversity of Chinese shrimp. The two different molecular biological methods gave similar results, but clone library analysis was more representative of the community to some extent. According to the two methods, Vibrio sp. was the predominant bacterial population in the intestine of Chinese shrimp.

Diversity of the bacterial community in the surface soil of a pear orchard based on 16S rRNA gene analysis.

A cultivation-independent approach based on polymerase chain reaction (PCR)-amplified partial small subunit rRNA genes was used to characterize bacterial populations in the surface soil of a commercial pear orchard consisting of different pear cultivars during two consecutive growing seasons. Pyrus communis L. cvs Blanquilla, Conference, and Williams are among the most widely cultivated cultivars in Europe and account for the majority of pear production in Northeastern Spain. To assess the heterogeneity of the community structure in response to environmental variables and tree phenology, bacterial populations were examined using PCR-denaturing gradient gel electrophoresis (DGGE) followed by cluster analysis of the 16S ribosomal DNA profiles by means of the unweighted pair group method with arithmetic means. Similarity analysis of the band patterns failed to identify characteristic fingerprints associated with the pear cultivars. Both environmentally and biologically based principal-component analyses showed that the microbial communities changed significantly throughout the year depending on temperature and, to a lesser extent, on tree phenology and rainfall. Prominent DGGE bands were excised and sequenced to gain insight into the identities of the predominant bacterial populations. Most DGGE band sequences were related to bacterial phyla, such as Bacteroidetes, Cyanobacteria, Acidobacteria, Proteobacteria, Nitrospirae, and Gemmatimonadetes, previously associated with typical agronomic crop environments.