scholarly journals Metagenomic analysis of microbial community in over-fermented tempeh

2019 ◽  
Vol 20 (4) ◽  
pp. 1106-1114 ◽  
Author(s):  
ARTINI PANGASTUTI ◽  
RIZAL KHOIRUN ALFISAH ◽  
NUR IFFAH ISTIANA ◽  
SITI LUSI ARUM SARI ◽  
RATNA SETYANINGSIH ◽  
...  
Keyword(s):  
Microbial Community ◽  
Relative Abundance ◽  
Kluyveromyces Marxianus ◽  
Functional Food ◽  
Nutritional Value ◽  
Fermentation Process ◽  
Starter Culture ◽  
Metagenomic Analysis ◽  
Candida Sp ◽  
Beneficial Effects

Abstract. Pangastuti A, Alfisah RK, Istiana NI, Sari SLA, Setyaningsih R, Susilowati A, Purwoko T. 2019. Metagenomic analysis of microbial community in over-fermented tempeh. Biodiversitas 20: 1106-1114. Tempeh is a traditional Indonesian food which is made from soybeans through a fermentation process using Rhizopus as a starter culture. Tempeh is now considered as a functional food with many beneficial effects to human health beyond its nutritional value. The microbial community during the further fermentation process of tempeh give typical characteristic taste and flavor. Therefore the over-fermented tempeh is used as a flavoring in some dishes. Metagenomic analysis needed to know the involvement of microbial communities since most of the microbes involved in further fermentation process are unculturable. This research aimed to study the diversity of the microbial community in the over-fermented tempeh (72 hours) using the metagenomic analysis. Seventeen OTUs of fungi in over-fermented tempeh were detected. Among them, 9 OTUs had significant abundance: six species were identified as Tryblidiopsis sichuanensis, Candida sp.2_1., Kluyveromyces marxianus, Trichosporon asahii, Trichosporon gracile, and Trichosporon ovoides, one species was identified in the order level Mucorales, and two fungi species could not be determined. Species of the order Mucorales was the dominant species in over-fermented tempeh (72 hours) with a relative abundance of 62.46%, followed by Kluyveromyces marxianus with a relative abundance of 3698%. Meanwhile, 132 OTUs of the bacterial community was detected, the predominant 10 genera were Chryseobacterium, Lactococcus, Lactobacillus, Streptococcus, Acetobacter, Novosphingobium, Comamonas, Escherichia, Klebsiella, and Stenotrophomonas, in which Lactobacillus agilis, Lactococcus sp., and Klebsiella sp., were most abundant with relative abundance of 27%, 26.3%, and 13% respectively.

scholarly journals StrainPro – a highly accurate Metagenomic strain-level profiling tool

2019 ◽  
Author(s):  
Hsin-Nan Lin ◽  
Yaw-Ling Lin ◽  
Wen-Lian Hsu
Keyword(s):  
Microbial Community ◽  
Relative Abundance ◽  
Taxonomic Diversity ◽  
Evaluation Study ◽  
Taxonomic Composition ◽  
Strain Level ◽  
Metagenomic Analysis ◽  
Reference Database ◽  
Analysis Tool ◽  
Analysis Tools

ABSTRACTCharacterizing the taxonomic diversity of a microbial community is very important to understand the roles of microorganisms. Next generation sequencing (NGS) provides great potential for investigation of a microbial community and leads to Metagenomic studies. NGS generates DNA fragment sequences directly from microorganism samples, and it requires analysis tools to identify microbial species (or taxonomic composition) and estimate their relative abundance in the studied community. However, only a few tools could achieve strain-level identification and most tools estimate the microbial abundances simply according to the read counts. An evaluation study on metagenomic analysis tools concludes that the predicted abundance differed significantly from the true abundance. In this study, we present StrainPro, a novel metagenomic analysis tool which is highly accurate both at characterizing microorganisms at strain-level and estimating their relative abundances. A unique feature of StrainPro is it identifies representative sequence segments from reference genomes. We generate three simulated datasets using known strain sequences and another three simulated datasets using unknown strain sequences. We compare the performance of StrainPro with seven existing tools. The results show that StrainPro not only identifies metagenomes with high precision and recall, but it is also highly robust even when the metagenomes are not included in the reference database. Moreover, StrainPro estimates the relative abundance with high accuracy. We demonstrate that there is a strong positive linear relationship between observed and predicted abundances.

scholarly journals Geothermal Gases Shape the Microbial Community of the Volcanic Soil of Pantelleria, Italy

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Nunzia Picone ◽  
Carmen Hogendoorn ◽  
Geert Cremers ◽  
Lianna Poghosyan ◽  
Arjan Pol ◽  
...  
Keyword(s):  
Microbial Community ◽  
Greenhouse Gas ◽  
Relative Abundance ◽  
Hot Spots ◽  
Microbial Community Composition ◽  
Metagenomic Analysis ◽  
Volcanic Soil ◽  
Metabolic Potential ◽  
Gas Emissions ◽  
Geothermal Activity

ABSTRACT Volcanic and geothermal environments are characterized by low pH, high temperatures, and gas emissions consisting of mainly CO2 and varied CH4, H2S, and H2 contents which allow the formation of chemolithoautotrophic microbial communities. To determine the link between the emitted gases and the microbial community composition, geochemical and metagenomic analysis were performed. Soil samples of the geothermic region Favara Grande (Pantelleria, Italy) were taken at various depths (1 to 50 cm). Analysis of the gas composition revealed that CH4 and H2 have the potential to serve as the driving forces for the microbial community. Our metagenomic analysis revealed a high relative abundance of Bacteria in the top layer (1 to 10 cm), but the relative abundance of Archaea increased with depth from 32% to 70%. In particular, a putative hydrogenotrophic methanogenic archaeon, related to Methanocella conradii, appeared to have a high relative abundance (63%) in deeper layers. A variety of [NiFe]-hydrogenase genes were detected, showing that H2 was an important electron donor for microaerobic microorganisms in the upper layers. Furthermore, the bacterial population included verrucomicrobial and proteobacterial methanotrophs, the former showing an up to 7.8 times higher relative abundance. Analysis of the metabolic potential of this microbial community showed a clear capacity to oxidize CH4 aerobically, as several genes for distinct particulate methane monooxygenases and lanthanide-dependent methanol dehydrogenases (XoxF-type) were retrieved. Analysis of the CO2 fixation pathways showed the presence of the Calvin-Benson-Bassham cycle, the Wood-Ljungdahl pathway, and the (reverse) tricarboxylic acid (TCA) cycle, the latter being the most represented carbon fixation pathway. This study indicates that the methane emissions in the Favara Grande might be a combination of geothermal activity and biological processes and further provides insights into the diversity of the microbial population thriving on CH4 and H2. IMPORTANCE The Favara Grande nature reserve on the volcanic island of Pantelleria (Italy) is known for its geothermal gas emissions and high soil temperatures. These volcanic soil ecosystems represent “hot spots” of greenhouse gas emissions. The unique community might be shaped by the hostile conditions in the ecosystem, and it is involved in the cycling of elements such as carbon, hydrogen, sulfur, and nitrogen. Our metagenome study revealed that most of the microorganisms in this extreme environment are only distantly related to cultivated bacteria. The results obtained profoundly increased the understanding of these natural hot spots of greenhouse gas production/degradation and will help to enrich and isolate the microbial key players. After isolation, it will become possible to unravel the molecular mechanisms by which they adapt to extreme (thermo/acidophilic) conditions, and this may lead to new green enzymatic catalysts and technologies for industry.

scholarly journals Salt concentration effect on yeast diversity of the Ivorian traditional fermented fish adjuevan

2020 ◽  
Vol 13 (1) ◽  
pp. 087-094
Author(s):  
Kouakou-Kouamé Amenan Clémentine ◽  
N guessan Kouadio Florent ◽  
Aka Solange ◽  
Montet Didier ◽  
Djè Koffi Marcellin
Keyword(s):  
Salt Concentration ◽  
Kluyveromyces Marxianus ◽  
Starter Culture ◽  
Yeast Identification ◽  
Fermented Fish ◽  
Torulaspora Delbrueckii ◽  
Yeast Diversity ◽  
Candida Sp ◽  
Traditional Fermentation ◽  
Candida Zeylanoides

This study aimed to investigate the yeast diversity in adjuevan fermented at the laboratory scale according to salt concentration following both traditional fermentation methods. Thus, the fish species Galeoides decadactylus was fermented with salt added at 10 %, 15 %, 20 %, 25 % and 30 % (w/w) for five days. Yeast identification using PCR-DDGE method reveled seven species which were Pichia fermentans, Candida zeylanoides, Candida sp, Hanseniaspora osmophila, Kluyveromyces sp; Torulaspora delbrueckii and Kluyveromyces marxianus. These species varied according to fermentation method used and salt concentration added with Pichia fermentans and Hanseniaspora osmophila as dominant strains. These results showed also that Kluyveromyces marxianus and Torulaspora delbrueckii were more tolerant to sodium chloride than the others. This work confirmed that yeasts were involved and participated in adjuevan production. Therefore, these yeasts should be tested for their functionality during the fermentation, and some might be useful as starter culture to produce better quality fermented fish adjuevan.

scholarly journals Probiyotik Mayalar ve Probiyotik Gıdalarda Mayaların Rolü

2019 ◽  
Vol 7 (9) ◽  
pp. 1268
Author(s):  
Eda Kılıç Kanak ◽  
Suzan Öztürk Yılmaz
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Kluyveromyces Marxianus ◽  
Nutritional Value ◽  
Yeast Species ◽  
Complex Compounds ◽  
Food Additive ◽  
Fermented Foods ◽  
Probiotic Properties ◽  
Organoleptic Properties ◽  
Beneficial Effects

Probiotics are defined as live microorganisms that provide beneficial effects when consumed in sufficient quantities. Currently available probiotics are bacteria such as Lactobacillus, Bifidobacterium and Bacillus. In recent years, yeast has presented great potential for the development of new probiotics. Saccharomyces cerevisiae var. boulardii is the only yeast that has been recognized and characterized as probiotic until today. This raises the question of whether other yeast species have probiotic properties. Recent investigations show that some species with probiotic evidence are Kluyveromyces marxianus and Pichia kudriavzeii, except S. cerevisiae. Most of the enzymes produced by the preserved yeast are involved in the metabolism of complex compounds in foods, thus forming the nutritional value and organoleptic properties of fermented foods. EFSA has given the QPS statue, the "food additive," only a few yeasts. In order to verify interesting properties, probiotic working of yeasts needs to be examined in more detail.

scholarly journals Impact of Fermentation Processes on the Bioactive Profile and Health-Promoting Properties of Bee Bread, Mead and Honey Vinegar

Processes ◽  
2020 ◽  
Vol 8 (9) ◽  
pp. 1081
Author(s):  
Rodica Mărgăoan ◽  
Mihaiela Cornea-Cipcigan ◽  
Erkan Topal ◽  
Mustafa Kösoğlu
Keyword(s):  
Fermentation Process ◽  
Starter Culture ◽  
Acid Fermentation ◽  
Lactic Fermentation ◽  
Beneficial Effects ◽  
Bee Bread ◽  
Health Promoting ◽  
Food Market ◽  
Medicinal Properties ◽  
Vital Resource

Recently, an increasing interest is paid to bee products obtained as a result of the fermentation process. Some of them can be consumed directly (bee-collected pollen, honey, bee bread etc.), while others are the result of lactic and/or acid fermentation (honey vinegar and honey wine). Bee bread is the result of pollens’ lactic fermentation, whereas mead is obtained by honeys’ lactic fermentation. Moreover, as a result of honey acetic acid fermentation, honey vinegar is obtained. Sensory characteristics and aroma composition have been scarcely studied, which may depend on the starter culture and fermentation process. Along with the medicinal properties they are a vital resource for future researches as they are of particular importance in the food market. In this review, we discuss the aroma-active compounds, taste, and sensorial characteristics of fermented bee products along with the approaches that can be developed for the flavor improvement based on existing technologies. Furthermore, the beneficial effects on human health are also described, with special attention that should be attributed to finding the use of probiotics in these fermented products as health-promoting effects.

Antidiabetic Properties of Medicinal Mushrooms with Special Reference to Phellinus Species: A Review

2020 ◽  
Vol 10 ◽  
Author(s):  
Thekkuttuparambil A Ajith ◽  
Kynoor K Janardhanan
Keyword(s):  
Nutritional Value ◽  
Modern Medicine ◽  
Lifestyle Changes ◽  
Controlled Clinical Trials ◽  
Chronic Complications ◽  
Medicinal Mushrooms ◽  
Beneficial Effects ◽  
First Line Therapy ◽  
Public Health Challenge ◽  
Microvascular Diseases

: Diabetes remains the major public health challenge to 21st century. It is strongly related to lifestyle changes. Most chronic complications of diabetes are macrovascular and microvascular diseases resulting from the existing hyperglycemic status. Failure of first line therapy which is based on diet modifications and exercise, conventional treatment using antihyperglycemic agents with different mechanisms of action will be implemented for type II diabetes in modern medicine. Higher Basidiomycetes mushrooms are highly praised for their nutritional value and pharmacological properties. They have long been used traditionally for the maintenance of health, prevention and treatment of various human ailments. Reports indicate the beneficial effects of medicinal mushrooms in diabetes treatments. However, scientific evidences are insufficient to make definitive conclusions on the efficacy of individual medicinal mushrooms. Mushrooms belong to the genera Phellinus such as Phellinus linteus, Phellinus ribis, Phellinus rimosus and Phellinus igniarius. They possess significant hypoglycemic effect in experimental diabetic models. However, well-designed controlled clinical trials are needed to establish their safety and bioactivity.

scholarly journals Current Trends in Enrichment of Wheat Pasta: Quality, Nutritional Value and Antioxidant Properties

Processes ◽  
2021 ◽  
Vol 9 (8) ◽  
pp. 1280
Author(s):  
Dariusz Dziki
Keyword(s):  
Shelf Life ◽  
Functional Food ◽  
Nutritional Value ◽  
Cooking Quality ◽  
Raw Materials ◽  
Antioxidant Properties ◽  
Healthy Foods ◽  
Simple Formulation ◽  
Cereal Products ◽  
Current Trends

Wheat pasta is one of the most important cereal products and is becoming increasingly popular worldwide because of its convenience, simple formulation, long shelf life, and high energetic value. Wheat pasta is usually obtained from refined flour rich in carbohydrates but with low content of phytochemicals, micronutrients, and fibre. The increased demand of consumers for healthy foods has generated interest among both researchers and food producers in developing functional food products. This review showcases the current trends in pasta fortification. Changes in the nutritional value, cooking quality, sensory attributes, and antioxidant properties of durum and common wheat pasta enriched with both plant and animal raw materials are discussed.

scholarly journals Pinus Species as Prospective Reserves of Bioactive Compounds with Potential Use in Functional Food—Current State of Knowledge

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1306
Author(s):  
Marcin Dziedziński ◽  
Joanna Kobus-Cisowska ◽  
Barbara Stachowiak
Keyword(s):  
Human Health ◽  
Bioactive Compounds ◽  
Functional Food ◽  
Biological Activities ◽  
Food Ingredients ◽  
Beneficial Effects ◽  
Pine Tree ◽  
Pine Trees ◽  
Health Promoting ◽  
Few Data

The pine (Pinus L.) is the largest and most heteromorphic plant genus of the pine family (Pinaceae Lindl.), which grows almost exclusively in the northern hemisphere. The demand for plant-based remedies, supplements and functional food is growing worldwide. Although pine-based products are widely available in many parts of the world, they are almost absent as food ingredients. The literature shows the beneficial effects of pine preparations on human health. Despite the wide geographical distribution of pine trees in the natural environment, there are very few data in the literature on the widespread use of pine in food technology. This study aims to present, characterise and evaluate the content of phytochemicals in pine trees, including shoots, bark and conifer needles, as well as to summarise the available data on their health-promoting and functional properties, and the potential of their use in food and the pharmaceutical industry to support health. Various species of pine tree contain different compositions of bioactive compounds. Regardless of the solvent, method, pine species and plant part used, all pine extracts contain a high number of polyphenols. Pine tree extracts exhibit several described biological activities that may be beneficial to human health. The available examples of the application of pine elements in food are promising. The reuse of residual pine elements is still limited compared to its potential. In this case, it is necessary to conduct more research to find and develop new products and applications of pine residues and by-products.

scholarly journals Effect of Thermal Processing on Color, Phenolic Compounds, and Antioxidant Activity of Faba Bean (Vicia faba L.) Leaves and Seeds

Antioxidants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1207
Author(s):  
Shu-Cheng Duan ◽  
Soon-Jae Kwon ◽  
Seok-Hyun Eom
Keyword(s):  
Antioxidant Activity ◽  
Faba Bean ◽  
Nutritional Value ◽  
Cooking Methods ◽  
Thermal Treatments ◽  
Nutritional Values ◽  
Beneficial Effects ◽  
Young Leaves ◽  
Dry Heating ◽  
Positive Correlations

The leaves and seeds of the faba bean are good sources of L-3,4-dihydroxyphenylalanin (L-dopa), and are usually eaten with thermal cooking methods. However, little information is available on the effect of thermal treatments on their nutritional value. We compared the changes in color, contents of L-dopa, vitamin C (Vc), total phenolics (TP), total flavonoids (TF) and antioxidant activity after dry heating or steaming faba bean leaves and seeds. The young leaves provided higher values of all the estimate factors, regardless of the thermal treatment. Steaming significantly degraded nutritional values of the leaves, but less changed in seeds, whereas dry heat maintained these attributes. The contents of L-dopa, Vc, TP and TF were shown to have strongly positive correlations with antioxidant activity in the leaves, whereas only L-dopa content was positively correlated with antioxidant activity of the seeds. Faba leaves contained relatively high L-dopa which possessed strong antioxidant activity compared to the Vc. As L-dopa is an important contributor to the antioxidant activity of faba leaves and seeds, consuming L-dopa from leaves may provide beneficial effects not only regarding Parkinson’s Disease.

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