Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food

ABSTRACTKimchi, a traditional food in the Korean culture, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation process. Metagenomic DNA was extracted from kimchi samples obtained periodically and was sequenced using a 454 GS FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera:Leuconostoc,Lactobacillus, andWeissella. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, theLeuconostoc mesenteroidessubsp.mesenteroidesATCC 8293 andLactobacillus sakeisubsp.sakei23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity toLeuconostoc mesenteroidesandLactobacillusgenes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophages during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.

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Defining the Functional Potential and Active Community Members of a Sediment Microbial Community in a High-Arctic Hypersaline Subzero Spring

Applied and Environmental Microbiology ◽

10.1128/aem.00153-13 ◽

2013 ◽

Vol 79 (12) ◽

pp. 3637-3648 ◽

Cited By ~ 31

Author(s):

Chih-Ying Lay ◽

Nadia C. S. Mykytczuk ◽

Étienne Yergeau ◽

Guillaume Lamarche-Gagnon ◽

Charles W. Greer ◽

...

Keyword(s):

Microbial Community ◽

Sulfur Metabolism ◽

Close Association ◽

High Arctic ◽

16S Rrna Genes ◽

Rrna Genes ◽

Metagenomic Data ◽

Metabolic Potential ◽

Data Set ◽

Content Type

ABSTRACTThe Lost Hammer (LH) Spring is the coldest and saltiest terrestrial spring discovered to date and is characterized by perennial discharges at subzero temperatures (−5°C), hypersalinity (salinity, 24%), and reducing (≈−165 mV), microoxic, and oligotrophic conditions. It is rich in sulfates (10.0%, wt/wt), dissolved H2S/sulfides (up to 25 ppm), ammonia (≈381 μM), and methane (11.1 g day−1). To determine its total functional and genetic potential and to identify its active microbial components, we performed metagenomic analyses of the LH Spring outlet microbial community and pyrosequencing analyses of the cDNA of its 16S rRNA genes. Reads related toCyanobacteria(19.7%),Bacteroidetes(13.3%), andProteobacteria(6.6%) represented the dominant phyla identified among the classified sequences. Reconstruction of the enzyme pathways responsible for bacterial nitrification/denitrification/ammonification and sulfate reduction appeared nearly complete in the metagenomic data set. In the cDNA profile of the LH Spring active community, ammonia oxidizers (Thaumarchaeota), denitrifiers (Pseudomonasspp.), sulfate reducers (Desulfobulbusspp.), and other sulfur oxidizers (Thermoprotei) were present, highlighting their involvement in nitrogen and sulfur cycling. Stress response genes for adapting to cold, osmotic stress, and oxidative stress were also abundant in the metagenome. Comparison of the composition of the functional community of the LH Spring to metagenomes from other saline/subzero environments revealed a close association between the LH Spring and another Canadian high-Arctic permafrost environment, particularly in genes related to sulfur metabolism and dormancy. Overall, this study provides insights into the metabolic potential and the active microbial populations that exist in this hypersaline cryoenvironment and contributes to our understanding of microbial ecology in extreme environments.

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Microbial Community Structure in Midgut and Hindgut of the Humus-Feeding Larva of Pachnoda ephippiata (Coleoptera: Scarabaeidae)

Applied and Environmental Microbiology ◽

10.1128/aem.69.11.6659-6668.2003 ◽

2003 ◽

Vol 69 (11) ◽

pp. 6659-6668 ◽

Cited By ~ 145

Author(s):

Markus Egert ◽

Bianca Wagner ◽

Thorsten Lemke ◽

Andreas Brune ◽

Michael W. Friedrich

Keyword(s):

Community Structure ◽

Microbial Community ◽

16S Rrna ◽

Companion Paper ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Polymorphism Analysis ◽

Gene Frequencies ◽

Fermentation Products

ABSTRACT The guts of soil-feeding macroinvertebrates contain a complex microbial community that is involved in the transformation of ingested soil organic matter. In a companion paper (T. Lemke, U. Stingl, M. Egert, M. W. Friedrich, and A. Brune, Appl. Environ. Microbiol. 69:6650-6658, 2003), we show that the gut of our model organism, the humivorous larva of the cetoniid beetle Pachnoda ephippiata, is characterized by strong midgut alkalinity, high concentrations of microbial fermentation products, and the presence of a diverse, yet unstudied microbial community. Here, we report on the community structure of bacteria and archaea in the midgut, hindgut, and food soil of P. ephippiata larvae, determined with cultivation-independent techniques. Clone libraries and terminal restriction fragment length polymorphism analysis of 16S rRNA genes revealed that the intestines of P. ephippiata larvae contain a complex gut microbiota that differs markedly between midgut and hindgut and that is clearly distinct from the microbiota in the food soil. The bacterial community is dominated by phylogenetic groups with a fermentative metabolism (Lactobacillales, Clostridiales, Bacillales, and Cytophaga-Flavobacterium-Bacteroides [CFB] phylum), which is corroborated by high lactate and acetate concentrations in the midgut and hindgut and by the large numbers of lactogenic and acetogenic bacteria in both gut compartments reported in the companion paper. Based on 16S rRNA gene frequencies, Actinobacteria dominate the alkaline midgut, while the hindgut is dominated by members of the CFB phylum. The archaeal community, however, is less diverse. 16S rRNA genes affiliated with mesophilic Crenarchaeota, probably stemming from the ingested soil, were most frequent in the midgut, whereas Methanobacteriaceae-related 16S rRNA genes were most frequent in the hindgut. These findings agree with the reported restriction of methanogenesis to the hindgut of Pachnoda larvae.

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Ultra-accurate microbial amplicon sequencing with synthetic long reads

Microbiome ◽

10.1186/s40168-021-01072-3 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Benjamin J. Callahan ◽

Dmitry Grinevich ◽

Siddhartha Thakur ◽

Michael A. Balamotis ◽

Tuval Ben Yehezkel

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Amplicon Sequencing ◽

Species Level ◽

Full Length ◽

16S Rrna Genes ◽

Rrna Genes ◽

Strain Identification ◽

Long Reads ◽

Long Read

Abstract Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. Methods Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. Results LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. Conclusions The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics.

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Habitat Elevation Shapes Microbial Community Composition and Alter the Metabolic Functions in Wild Sable (Martes zibellina) Guts

Animals ◽

10.3390/ani11030865 ◽

2021 ◽

Vol 11 (3) ◽

pp. 865

Author(s):

Lantian Su ◽

Xinxin Liu ◽

Guangyao Jin ◽

Yue Ma ◽

Haoxin Tan ◽

...

Keyword(s):

Microbial Community ◽

Environmental Factors ◽

Microbial Communities ◽

Community Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Functional Genes ◽

Martes Zibellina ◽

Clear Cutting ◽

Metabolic Functions

In recent decades, wild sable (Carnivora Mustelidae Martes zibellina) habitats, which are often natural forests, have been squeezed by anthropogenic disturbances such as clear-cutting, tilling and grazing. Sables tend to live in sloped areas with relatively harsh conditions. Here, we determine effects of environmental factors on wild sable gut microbial communities between high and low altitude habitats using Illumina Miseq sequencing of bacterial 16S rRNA genes. Our results showed that despite wild sable gut microbial community diversity being resilient to many environmental factors, community composition was sensitive to altitude. Wild sable gut microbial communities were dominated by Firmicutes (relative abundance 38.23%), followed by Actinobacteria (30.29%), and Proteobacteria (28.15%). Altitude was negatively correlated with the abundance of Firmicutes, suggesting sable likely consume more vegetarian food in lower habitats where plant diversity, temperature and vegetation coverage were greater. In addition, our functional genes prediction and qPCR results demonstrated that energy/fat processing microorganisms and functional genes are enriched with increasing altitude, which likely enhanced metabolic functions and supported wild sables to survive in elevated habitats. Overall, our results improve the knowledge of the ecological impact of habitat change, providing insights into wild animal protection at the mountain area with hash climate conditions.

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Variability of the Sheep Lung Microbiota

Applied and Environmental Microbiology ◽

10.1128/aem.00540-16 ◽

2016 ◽

Vol 82 (11) ◽

pp. 3225-3238 ◽

Cited By ~ 27

Author(s):

Laura Glendinning ◽

Steven Wright ◽

Jolinda Pollock ◽

Peter Tennant ◽

David Collie ◽

...

Keyword(s):

Spatial Variability ◽

Dna Sequences ◽

Bacterial Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Large Animal ◽

Local Factors ◽

Adult Sheep ◽

Sequencing Technologies ◽

Host Influence

ABSTRACTSequencing technologies have recently facilitated the characterization of bacterial communities present in lungs during health and disease. However, there is currently a dearth of information concerning the variability of such data in health both between and within subjects. This study seeks to examine such variability using healthy adult sheep as our model system. Protected specimen brush samples were collected from three spatially disparate segmental bronchi of six adult sheep (age, 20 months) on three occasions (day 0, 1 month, and 3 months). To further explore the spatial variability of the microbiotas, more-extensive brushing samples (n= 16) and a throat swab were taken from a separate sheep. The V2 and V3 hypervariable regions of the bacterial 16S rRNA genes were amplified and sequenced via Illumina MiSeq. DNA sequences were analyzed using the mothur software package. Quantitative PCR was performed to quantify total bacterial DNA. Some sheep lungs contained dramatically different bacterial communities at different sampling sites, whereas in others, airway microbiotas appeared similar across the lung. In our spatial variability study, we observed clustering related to the depth within the lung from which samples were taken. Lung depth refers to increasing distance from the glottis, progressing in a caudal direction. We conclude that both host influence and local factors have impacts on the composition of the sheep lung microbiota.IMPORTANCEUntil recently, it was assumed that the lungs were a sterile environment which was colonized by microbes only during disease. However, recent studies using sequencing technologies have found that there is a small population of bacteria which exists in the lung during health, referred to as the “lung microbiota.” In this study, we characterize the variability of the lung microbiotas of healthy sheep. Sheep not only are economically important animals but also are often used as large animal models of human respiratory disease. We conclude that, while host influence does play a role in dictating the types of microbes which colonize the airways, it is clear that local factors also play an important role in this regard. Understanding the nature and influence of these factors will be key to understanding the variability in, and functional relevance of, the lung microbiota.

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Subsoil microbial community responses to air exposure and legume growth depend on soil properties across different depths

Scientific Reports ◽

10.1038/s41598-019-55089-8 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Hongmei Yan ◽

Fan Yang ◽

Jiamin Gao ◽

Ziheng Peng ◽

Weimin Chen

Keyword(s):

Microbial Community ◽

Soil Properties ◽

16S Rrna Genes ◽

Rrna Genes ◽

Soil Profiles ◽

Air Exposure ◽

Structure Variation ◽

Α Diversity ◽

Different Depths ◽

Legume Growth

AbstractAnthropogenic disturbance, such as agricultural and architectural activities, can greatly influence belowground soil microbes, and thus soil formation and nutrient cycling. The objective of this study was to investigate microbial community variation in deep soils affected by strong disturbances. In present study, twelve soil samples were collected from different depths (0–300 cm) and placed onto the surface. We investigated the structure variation of the microbial community down through the soil profiles in response to disturbance originated by legume plants (robinia and clover) cultivation vs. plant-free controls. The high-throughput sequencing of 16S rRNA genes showed that microbial α-diversity decreased with depth, and that growing both plants significantly impacted the diversity in the topsoil. The soil profile was clustered into three layers: I (0–40 cm), II (40–120 cm), and III (120–300 cm); with significantly different taxa found among them. Soil properties explained a large amount of the variation (23.5%) in the microbial community, and distinct factors affected microbial assembly in the different layers, e.g., available potassium in layer I, pH and total nitrogen in layer II, pH and organic matter in layer III. The prediction of metabolic functions and oxygen requirements indicated that the number of aerobic bacteria increased with more air exposure, which may further accelerate the transformation of nitrogen, sulfur, carbon, and pesticides in the soil. The diversity of soil microorganisms followed a depth-decay pattern, but became higher following legume growth and air exposure, with notable abundance variation of several important bacterial species, mainly belonging to Nitrospira, Verrucomicrobia, and Planctomycetes, and soil properties occurring across the soil profiles.

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Abundance and Microbial Diversity from Surface to Deep Water Layers Over the Rio Grande Rise, South Atlantic

10.1101/2021.04.22.441028 ◽

2021 ◽

Author(s):

Juliana Correa Neiva Ferreira ◽

Natascha M. Bergo ◽

Pedro M. Tura ◽

Mateus Gustavo Chuqui ◽

Frederico P. Brandini ◽

...

Keyword(s):

Microbial Community ◽

Microbial Diversity ◽

Rio Grande ◽

South Atlantic ◽

Water Masses ◽

16S Rrna Genes ◽

Rrna Genes ◽

List Type ◽

Tropical Water ◽

Southwestern Atlantic Ocean

AbstractMarine microbes control the flux of matter and energy essential for life in the oceans. Until now, the distribution and diversity of planktonic microorganisms above Fe-Mn crusts has received relatively little attention. Future mining\dredging of these minerals is predicted to affect microbial diversity and functioning in the deep sea. Here, we studied the ecology of planktonic microbes among pelagic environments of an Fe-Mn deposit region, at Rio Grande Rise, Southwestern Atlantic Ocean. We investigated microbial community composition using high-throughput sequencing of 16S rRNA genes and their abundance estimated by flow cytometry. Our results showed that the majority of picoplanktonic was found in epi- and mesopelagic waters, corresponding to the Tropical Water and South Atlantic Central Water. Bacterial and archaeal groups related to phototrophy, heterotrophy and chemosynthesis, such as Synechococcales, Sar11 (Proteobacteria) and Nitrosopumilales (Thaumarchaeota) were the main representatives of the pelagic microbial community. Additionally, we detected abundant assemblages involved in biodegradation of marine organic matter and iron oxidation at deep waters, i.e., Pseudoalteromonas and Alteromonas. No differences were observed in microbial community alpha diversity. However, we detected differences in community structure between water masses, suggesting that changes in an environmental setting (i.e. nutrient availability or circulation) play a significant role in structuring the pelagic zones, also affecting the meso- and bathypelagic microbiome.HighlightsRio Grande Rise pelagic microbiomePicoplankton carbon biomass partitioning through pelagic zonesUnique SAR11 Clade I oligotype in the shallowest Tropical WaterHigher number of shared oligotypes between deepest water massesNitrogen, carbon and sulfur may be important contributors for the pelagic microbiome

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Biphenyl-Metabolizing Bacteria in the Rhizosphere of Horseradish and Bulk Soil Contaminated by Polychlorinated Biphenyls as Revealed by Stable Isotope Probing

Applied and Environmental Microbiology ◽

10.1128/aem.00466-09 ◽

2009 ◽

Vol 75 (20) ◽

pp. 6471-6477 ◽

Cited By ~ 68

Author(s):

Ondrej Uhlik ◽

Katerina Jecna ◽

Martina Mackova ◽

Cestmir Vlcek ◽

Miluse Hroudova ◽

...

Keyword(s):

Microbial Community ◽

Stable Isotope ◽

Polychlorinated Biphenyls ◽

Stable Isotope Probing ◽

Amino Acid Sequences ◽

16S Rrna Genes ◽

Bulk Soil ◽

Rrna Genes ◽

Soil Environment ◽

Α Subunits

ABSTRACT DNA-based stable isotope probing in combination with terminal restriction fragment length polymorphism was used in order to identify members of the microbial community that metabolize biphenyl in the rhizosphere of horseradish (Armoracia rusticana) cultivated in soil contaminated with polychlorinated biphenyls (PCBs) compared to members of the microbial community in initial, uncultivated bulk soil. On the basis of early and recurrent detection of their 16S rRNA genes in clone libraries constructed from [13C]DNA, Hydrogenophaga spp. appeared to dominate biphenyl catabolism in the horseradish rhizosphere soil, whereas Paenibacillus spp. were the predominant biphenyl-utilizing bacteria in the initial bulk soil. Other bacteria found to derive carbon from biphenyl in this nutrient-amended microcosm-based study belonged mostly to the class Betaproteobacteria and were identified as Achromobacter spp., Variovorax spp., Methylovorus spp., or Methylophilus spp. Some bacteria that were unclassified at the genus level were also detected, and these bacteria may be members of undescribed genera. The deduced amino acid sequences of the biphenyl dioxygenase α subunits (BphA) from bacteria that incorporated [13C]into DNA in 3-day incubations of the soils with [13C]biphenyl are almost identical to that of Pseudomonas alcaligenes B-357. This suggests that the spectrum of the PCB congeners that can be degraded by these enzymes may be similar to that of strain B-357. These results demonstrate that altering the soil environment can result in the participation of different bacteria in the metabolism of biphenyl.

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Bacterial Diversity and Function of Aerobic Granules Engineered in a Sequencing Batch Reactor for Phenol Degradation

Applied and Environmental Microbiology ◽

10.1128/aem.70.11.6767-6775.2004 ◽

2004 ◽

Vol 70 (11) ◽

pp. 6767-6775 ◽

Cited By ~ 98

Author(s):

He-Long Jiang ◽

Joo-Hwa Tay ◽

Abdul Majid Maszenan ◽

Stephen Tiong-Lee Tay

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Bacterial Diversity ◽

Sequencing Batch Reactor ◽

Batch Reactor ◽

Phenol Degradation ◽

16S Rrna Genes ◽

Rrna Genes ◽

Aerobic Granules ◽

And Function

ABSTRACT Aerobic granules are self-immobilized aggregates of microorganisms and represent a relatively new form of cell immobilization developed for biological wastewater treatment. In this study, both culture-based and culture-independent techniques were used to investigate the bacterial diversity and function in aerobic phenol- degrading granules cultivated in a sequencing batch reactor. Denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA genes demonstrated a major shift in the microbial community as the seed sludge developed into granules. Culture isolation and DGGE assays confirmed the dominance of β-Proteobacteria and high-G+C gram-positive bacteria in the phenol-degrading aerobic granules. Of the 10 phenol-degrading bacterial strains isolated from the granules, strains PG-01, PG-02, and PG-08 possessed 16S rRNA gene sequences that matched the partial sequences of dominant bands in the DGGE fingerprint belonging to the aerobic granules. The numerical dominance of strain PG-01 was confirmed by isolation, DGGE, and in situ hybridization with a strain-specific probe, and key physiological traits possessed by PG-01 that allowed it to outcompete and dominate other microorganisms within the granules were then identified. This strain could be regarded as a functionally dominant strain and may have contributed significantly to phenol degradation in the granules. On the other hand, strain PG-08 had low specific growth rate and low phenol degradation ability but showed a high propensity to autoaggregate. By analyzing the roles played by these two isolates within the aerobic granules, a functional model of the microbial community within the aerobic granules was proposed. This model has important implications for rationalizing the engineering of ecological systems.

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Bioaugmentation of Activated Sludge by an Indigenous 3-Chloroaniline-Degrading Comamonas testosteroni Strain, I2gfp

Applied and Environmental Microbiology ◽

10.1128/aem.66.7.2906-2913.2000 ◽

2000 ◽

Vol 66 (7) ◽

pp. 2906-2913 ◽

Cited By ~ 249

Author(s):

Nico Boon ◽

Johan Goris ◽

Paul De Vos ◽

Willy Verstraete ◽

Eva M. Top

Keyword(s):

Community Structure ◽

Microbial Community ◽

Activated Sludge ◽

Microbial Community Structure ◽

Denaturing Gradient Gel Electrophoresis ◽

Dynamic Change ◽

16S Rrna Genes ◽

Rrna Genes ◽

Adaptation Period ◽

Comamonas Testosteroni

ABSTRACT A strain identified as Comamonas testosteroni I2 was isolated from activated sludge and found to be able to mineralize 3-chloroaniline (3-CA). During the mineralization, a yellow intermediate accumulated temporarily, due to the distalmeta-cleavage of chlorocatechol. This strain was tested for its ability to clean wastewater containing 3-CA upon inoculation into activated sludge. To monitor its survival, the strain was chromosomally marked with the gfp gene and designated I2gfp. After inoculation into a lab-scale semicontinuous activated-sludge (SCAS) system, the inoculated strain maintained itself in the sludge for at least 45 days and was present in the sludge flocs. After an initial adaptation period of 6 days, complete degradation of 3-CA was obtained during 2 weeks, while no degradation at all occurred in the noninoculated control reactor. Upon further operation of the SCAS system, only 50% 3-CA removal was observed. Denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes revealed a dynamic change in the microbial community structure of the activated sludge. The DGGE patterns of the noninoculated and the inoculated reactors evolved after 7 days to different clusters, which suggests an effect of strain inoculation on the microbial community structure. The results indicate that bioaugmentation, even with a strain originating from that ecosystem and able to effectively grow on a selective substrate, is not permanent and will probably require regular resupplementation.

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