scholarly journals Mining the evolutionary patterns of pit mud microbiome and driving factors under the impact of long-term strong-flavor baijiu production

Author(s):  
Li-Juan Chai ◽  
Wei Qian ◽  
Xiao-Zhong Zhong ◽  
Xiao-Juan Zhang ◽  
Zhen-Ming Lu ◽  
...  

Mud cellar creates a unique microenvironment for the fermentation of strong-flavor baijiu (SFB). Recent researches and long-term practice have highlighted the key roles of microbes inhabiting pit mud in the formation of SFB’s characteristic flavor. A positive correlation between the quality of SFB and cellar age was extracted from practice, however, the evolutionary patterns of pit mud microbiome and driving factors remain unclear. Here, based on the variation regularity analysis of microbial community structure and metabolites of samples from cellars of different ages (∼30/100/300 years), we further investigated the effects of lactate and acetate (main microbial metabolites in fermented grains) on modulating pit mud microbiome. Esters (50.3%-64.5%) dominated the volatile compounds identified in pit mud, and contents of the four typical acids (lactate, hexanoate, acetate and butyrate) increased with cellar age. Bacteria (9.5-10.4 lg copies/g) and archaea (8.3-9.1 lg copies/g) mainly constituted pit mud microbiota, respectively dominated by Clostridia (39.7%-81.2%) and Methanomicrobia (32.8%-92.9%). An upward trend with cellar age characterized the relative and absolute abundance of the most predominant bacterial/archaeal genus, Caproiciproducens / Methanosarcina . Correlation analysis revealed significantly ( P < 0.05) positive relationships between the two genera and major metabolites. Anaerobic fermentation with acetate and lactate as carbon sources enhanced the enrichment of Clostridia, and furthermore, the relative abundance of Caproiciproducens (40.9%) significantly increased after 15-day fed-batch fermentation with lactate compared with the initial pit mud (0.22%). This work presents a directional evolutionary pattern of pit mud microbial consortia and provides an alternative way to accelerate the enrichment of functional microbes. Importance The solid-state anaerobic fermentation in a mud cellar is the most typical feature of strong-flavor baijiu (SFB). Metabolites produced by microbes inhabiting pit mud are crucial to create the unique flavor of SFB. Accordingly, craftspeople have always highlighted the importance of pit mud microbiome and concluded by centuries of practice that the production rate of high-quality baijiu increases with cellar age. To deepen the understanding of pit mud microbiome, we determined the microbial community and metabolites of different-aged pit mud, inferred the main functional groups and explored the forces driving the microbial community evolution through metagenomic, metabolomic and multivariate statistical analyses. The results showed that the microbial consortia of pit mud presented a regular and directional evolutionary pattern under the impact of continuously batch-to-batch brewing activities. This work provides insight into the key roles of pit mud microbiome in SFB production and supports the production optimization of high-quality pit mud.

Metabolites ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 93 ◽  
Author(s):  
Cora McHugh ◽  
Thomas Flott ◽  
Casey Schooff ◽  
Zyad Smiley ◽  
Michael Puskarich ◽  
...  

Background: Though blood is an excellent biofluid for metabolomics, proteins and lipids present in blood can interfere with 1d-1H NMR spectra and disrupt quantification of metabolites. Here, we present effective macromolecule removal strategies for serum and whole blood (WB) samples. Methods: A variety of macromolecule removal strategies were compared in both WB and serum, along with tests of ultrafiltration alone and in combination with precipitation methods. Results: In healthy human serum, methanol:chloroform:water extraction with ultrafiltration was compared to methanol precipitation with and without ultrafiltration. Methods were tested in healthy pooled human serum, and in serum from patients with sepsis. Effects of long-term storage at −80 °C were tested to explore the impact of macromolecule removal strategy on serum from different conditions. In WB a variety of extraction strategies were tested in two types of WB (from pigs and baboons) to examine the impact of macromolecule removal strategies on different samples. Conclusions: In healthy human serum methanol precipitation of serum with ultrafiltration was superior, but was similar in recovery and variance to methanol:chloroform:water extraction with ultrafiltration in pooled serum from patients with sepsis. In WB, high quality, quantifiable spectra were obtained with the use of a methanol: chloroform precipitation.


mSystems ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Karoline Faust

ABSTRACT The investigation of microbial community dynamics is hampered by low resolution, a lack of control, and a small number of replicates. These deficiencies can be tackled with defined communities grown under well-controlled conditions in high-throughput automated cultivation devices. Besides delivering high-quality microbial community data, automated cultivation will also ease measurement of the basic parameters needed to parameterize mathematical models of microbial communities. Better experimental data will allow revisiting classical ecological questions, such as the impact of community structure on dynamics. In addition, such data will allow validation and comparison of community models and benchmarking of microbial data analysis software. In summary, high-throughput automated cultivation will lead to a deeper understanding of microbial community dynamics through better models and software.


2021 ◽  
Author(s):  
Jinjing Lu ◽  
Shengping Li ◽  
Guopeng Liang ◽  
Xueping Wu ◽  
Qiang Zhang ◽  
...  

Abstract Long term fertilization alters soil microbiological properties and then affects soil organic carbon (SOC) stocks. However, the interrelations of SOC with biological drivers and their relative importance are rarely analyzed quantitatively at aggregate scale. We investigated the contribution of soil microbial biomass, diversity and enzyme activity to C stock in soil aggregate fractions (> 5 mm, 2 − 5 mm, 1 − 2 mm, 0.25 − 1 mm and < 0.25 mm) at topsoil (0–15 cm) from 27-year long term fertilization regime. Compared to CK (no fertilization management), NPS and NPM (inorganic fertilization plus the incorporation of maize straw or composted cow manure) significantly reduced the impact of NP (inorganic fertilizers application alone) on the growth of microbial community, and increased the microbial contribution to C stock. The results showed that microbial variables were significantly correlated with SOC content in > 0.25 mm aggregates rather than in < 0.25 mm aggregates. Fungal variables (fungal, AM biomass, and F/B ratio) and enzyme activities (BXYL and LAP) in > 0.25 mm aggregates explained 21% and 2% on C, respectively. Overall, organic matter (OM) addition could contribute to higher C storage by boosting fungal community and enzyme activity rather than by changing microbial community diversity in macro-aggregates.


2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Sally L. Bornbusch ◽  
Rachel L. Harris ◽  
Nicholas M. Grebe ◽  
Kimberly Roche ◽  
Kristin Dimac-Stohl ◽  
...  

Abstract Background Antibiotics alter the diversity, structure, and dynamics of host-associated microbial consortia, including via development of antibiotic resistance; however, patterns of recovery from microbial imbalances and methods to mitigate associated negative effects remain poorly understood, particularly outside of human-clinical and model-rodent studies that focus on outcome over process. To improve conceptual understanding of host-microbe symbiosis in more naturalistic contexts, we applied an ecological framework to a non-traditional, strepsirrhine primate model via long-term, multi-faceted study of microbial community structure before, during, and following two experimental manipulations. Specifically, we administered a broad-spectrum antibiotic, either alone or with subsequent fecal transfaunation, to healthy, male ring-tailed lemurs (Lemur catta), then used 16S rRNA and shotgun metagenomic sequencing to longitudinally track the diversity, composition, associations, and resistomes of their gut microbiota both within and across baseline, treatment, and recovery phases. Results Antibiotic treatment resulted in a drastic decline in microbial diversity and a dramatic alteration in community composition. Whereas microbial diversity recovered rapidly regardless of experimental group, patterns of microbial community composition reflected long-term instability following treatment with antibiotics alone, a pattern that was attenuated by fecal transfaunation. Covariation analysis revealed that certain taxa dominated bacterial associations, representing potential keystone species in lemur gut microbiota. Antibiotic resistance genes, which were universally present, including in lemurs that had never been administered antibiotics, varied across individuals and treatment groups. Conclusions Long-term, integrated study post antibiotic-induced microbial imbalance revealed differential, metric-dependent evidence of recovery, with beneficial effects of fecal transfaunation on recovering community composition, and potentially negative consequences to lemur resistomes. Beyond providing new perspectives on the dynamics that govern host-associated communities, particularly in the Anthropocene era, our holistic study in an endangered species is a first step in addressing the recent, interdisciplinary calls for greater integration of microbiome science into animal care and conservation.


2021 ◽  
Vol 12 ◽  
Author(s):  
Silvia Juliana Martinez ◽  
João Batista Pavesi Simão ◽  
Victor Satler Pylro ◽  
Rosane Freitas Schwan

Coffee harvested in the Caparaó region (Minas Gerais, Brazil) is associated with high-quality coffee beans resulting in high-quality beverages. We characterize, microbiologically and chemically, fermented coffees from different altitudes through target NGS, chromatography, and conventional chemical assays. The genera Gluconobacter and Weissella were dominant in coffee’s fruits from altitudes 800 and 1,000 m. Among the Eukaryotic community, yeasts were the most dominant in all altitudes. The most dominant fungal genus was Cystofilobasidium, which inhabits cold environments and resists low temperatures. The content of acetic acid was higher at altitudes 1,200 and 1,400 m. Lactic acid and the genus Leuconostoc (Pearson: 0.93) were positively correlated. The relative concentration of volatile alcohols, especially of 2-heptanol, was high at all altitudes. Bacteria population was higher in coffees from 800 m, while at 1,000 m, fungi richness was favored. The altitude is an important variable that caused shifts in the microbial community and biochemical compounds content, even in coffees belonging to the same variety and cultivated in the same region under SIAF (self-induced anaerobic fermentation) conditions. Coffee from lower altitudes has higher volatile alcohols content, while high altitudes have esters, aldehydes, and total phenolics contents.


Author(s):  
А.А. Кутузова ◽  
Д.М. Тебердиев ◽  
В.М. Косолапов ◽  
Л.С. Трофимова ◽  
А.В. Родионова ◽  
...  

Исследования проводили в ФНЦ «ВИК им. В. Р. Вильямса» на базе трёх долголетних полевых экспериментов: в опыте 1 изучали многоукосное использование ранних и среднеспелых злаковых травостоев в среднем за 28 лет (1993–2020 годы), в опыте 2 — люцерно-злаковые травостои для позднего звена укосного конвейера в среднем за 7 лет пользования (2013–2020 годы), в опыте 3 проведено сравнение четырёх технологических систем создания и использования травостоев за последние 28 лет (в среднем за 47–74-й годы пользования, 1993–2020 годы). Цель исследований — определение агроэнергетической эффективности 15 технологий по созданию усовершенствованных злаковых и бобово-злаковых травостоев, а также шести систем ведения долголетних сенокосов при производстве сырья для заготовки высококачественного сена и сенажа. Применение нового метода агроэнергетической оценки антропогенных затрат не только подтверждает высокую экономическую эффективность создания сеяных травостоев на лугах, но и впервые в конкретных (цифровых) показателях устанавливает роль разнообразных природных факторов. На долголетних злаковых травостоях (в течение 28 лет жизни трав) обеспечивается производство сырьевой массы для заготовки объёмистых кормов (сена и сенажа) первого и второго классов. Совокупные антропогенные затраты энергии на этих травостоях в среднем за 28 лет составили 16,3–17,1 ГДж/га при двухукосной и 23,2–23,6 ГДж/га — при трёхукосной технологии, на люцерно-злаковых травостоях при двух укосах в среднем за 7 лет — 5,2–5,8 ГДж/га. Затраты окупались сбором обменной энергии на ранних и среднеспелых агроценозах с доминированием корневищных злаковых видов в 2,8–3,3 раза, а на люцерно-злаковых травостоях — в 10,6–11,0 раз. В структуре производства обменной энергии основная её часть обеспечивалась за счёт возобновляемых природных факторов: 67–70% — на злаковых травостоях и 90% — на бобово-злаковых долголетних травостоях. The research took place at the Federal Williams Research Center of Fodder Production and Agroecology and consisted of three long-term field trials. The trial 1 was aimed at studying the multi-cut use of short- and mid-season gramineous for 28 years (1993–2020). The trial 2 tested alfalfa-gramineous swards for late cutting for 7 years (2013–2020). The trial 3 compared four technological systems of sward development and cultivation for the last 28 years (1993–2020). The aim of this research was to determine the energy efficiency of 15 cultivation technologies for optimization of gramineous and legume-gramineous swards as well as six systems of long-term hayfield cultivation to obtain high-quality hay and haylage. New method evaluating anthropogenic costs proved high economic efficiency of sown swards but also showed the impact of various natural factors. Long-term gramineous swards (28 years of life) provided raw material for bulk feed production (hay and haylage) of the first and second grade. For such swards total anthropogenic costs amounted to 16.3–17.1 GJ ha-1 under two cuts and 23.2–23.6 GJ ha-1 — under three cuts for 28 years. For alfalfa-gramineous swards total anthropogenic costs amounted to 5.2–5.8 GJ ha-1 for 7 years. The costs were paid back by 2.8–3.3 times through the exchange energy yield from short- and mid-season ecosystems with higher proportion of rootstock grasses, from alfalfa-gramineous swards — by 10.6–11.0 times. The great part of exchange energy was provided through renewable natural factors: 67–70% — from gramineous swards and 90% — from the legume-gramineous ones.


2001 ◽  
Vol 1 ◽  
pp. 500-504 ◽  
Author(s):  
Teri C. Balser

We evaluated the microbial communities in three Hawaiian forest soils along a natural fertility gradient and compared their distinct responses to long-term nitrogen (N) additions. The sites studied have the same elevation, climate, and dominant vegetation, but vary in age of development, and thus in soil nutrient availability and nutrient limitation to plant growth. Fertilized plots at each site have received 100 kg ha year-1N addition for at least 8 years. Soil parameters, water content, pH, and ammonium and nitrate availability differed by site, but not between control and N-addition treatments within a site at the time of sampling. Microbial biomass also varied by site, but was not affected by N addition. In contrast, microbial community composition (measured by phospholipid analysis) varied among sites and between control and N-addition plots within a site. These data suggest that microbial community composition responds to N addition even when plant net primary productivity is limited by nutrients other than N. This may have implications for the behavior of forests impacted by atmospheric N deposition that are considered to be “nitrogen saturated,” yet still retain N in the soil.


2017 ◽  
Vol 10 (1) ◽  
pp. 87-99
Author(s):  
Aleksi Karhula ◽  
Hannu Lehti ◽  
Jani Erola

We studied the intergenerational impact of parental unemployment on the socioeconomic status of children. We used data from the Finnish depression of the 1990s, one of the deepest depressions in the history of OECD countries. We compared the impact of parental unemployment of children aged 12-18 during both a period of economic growth and a period of depression. We used ISEI status to measure social status when the children reached the age of 30. We used propensity score matching to analyse the high-quality Finnish register data, comprising 15991 children. Our results show a negative association between parental unemployment and children’s later socioeconomic status that is not significantly lower when parental unemployment occurs during a depression. The association is partially driven by the duration of unemployment during the depression. Our results underline the importance of providing support to families that experience parental unemployment during eras of both depression and growth.


Author(s):  
Huilin Wang ◽  
Yang Gu ◽  
Weicheng Zhou ◽  
Dong Zhao ◽  
Zongwei Qiao ◽  
...  

The transformation of diverse feedstocks into medium-chain fatty acids (MCFAs) by mixed cultures is a promising biorefinery route because of the high value of MCFAs. A particular concern is how to maintain the microbial consortia in mixed cultures to achieve stable MCFA production. Chinese strong aroma-type liquor ( Baijiu ) fermentation system continually produces caproic acid for decades through a spontaneous inoculation of anaerobes from pit mud into fermented grains. Therefore, illuminating the dominant caproate-producing bacterium (CPB) in pit mud and how the CPB sustains in the spontaneous fermentation system will benefit to reveal the microbiological mechanisms of the stable caproate production. Here, we examined pit mud samples across four Chinese strong aroma-type Baijiu producing areas and found that a caproate-producing Caproicibacterium sp. was widely distributed in these distilleries with relative abundance ranging from 1.4% to 35.5% and an average abundance of 11.4%. Through controlling carbon source availability, we achieved different simplified caproate-producing consortia and found that the growth advantage of Caproicibacterium sp. was highly dependent on glucose. Then two strains, named Caproicibacterium sp. LBM19010 and Caproicibacterium sp. JNU-WLY1368, were isolated from pit mud of two regions. The metabolic versatility of this bacterium utilizing starch, maltose, glucose and lactate reflected its adaptability to the fermentation environment where these carbon sources coexist. The simultaneous utilization of glucose and lactate contributed to the balance between cell growth and pH homeostasis. This study reveals that multiple adaptation strategies employed by the predominant CPB promotes its stability and dominance in a saccharide- and lactate-rich anaerobic habitat. IMPORTANCE Chinese strong aroma-type liquor ( Baijiu ) fermentation environment is a typical medium-chain fatty acid producing system with complex nutrients. Although several studies have revealed the correlation between microbial community composition and abiotic factors, the adaptation mechanisms of dominant species to abiotic environment are still unknown in this special anaerobic habitat. This study identified the predominant CPB in Chinese strong aroma-type Baijiu fermentation system. Metabolic versatility and flexibility of the dominant CPB with a small-size genome indicated that this bacterium can effectively exploit available carbon and nitrogen sources, which could be a key factor to promote its ecological success in a multi-species environment. The understanding of growth and metabolic features of CPB responsible for its dominance in microbial community will not only contribute to the improvement of Chinese strong aroma-type Baijiu production but also expand its potential industrial applications in caproate production.


2016 ◽  
Vol 2 (5) ◽  
pp. 239
Author(s):  
R.N Sugitha Nadarajah

<p>The journal of Advances in Modern Oncology Research (AMOR) is proud to announce its partnership with Portico, a leading digital preservation service provider, to ensure the long term accessibility of its published contents. In addition, it is now indexed by the gold standard of chemical information database Chemical Abstracts Services (CAS) after publishing only six bimonthly issues, dating back to October 2015. AMOR’s Editor-in-Chief Dr. Omar Abdel-Rahman proudly shares: “Our vision is to be far more than just a journal, we want to be a platform that publishes high quality cancer research contents from all over the world. I think we are progressing, at an acceptable pace, in that direction."</p><p> </p><p>The Portico archive is a “centralized repository of tens of thousands of e-journals, e-books, and other electronic content, replicated to ensure security,” according to the registry organization. “Content comes into the archive under formal preservation agreements with publishers. Content providers submit source files to Portico, and we repackage these source files into an archival format and provide long-term archival management and format migration as needed. Our approach is driven by our commitment to meeting clear preservation goals,” it states. </p><p> </p><p>AMOR’s Managing Editor Dr. TS Jong, when asked to comment about the impact of this development, adds: “AMOR is committed towards meeting the highest international publication standards and as such, has a clear archiving and indexing roadmap to sustain our growth. The journal acknowledges the importance of ensuring the continuous accessibility of our published articles in multiple repositories. Therefore, we are delighted with the recent partnership between AMOR and Portico, a well-known third-party repository service provider, to safeguard the long-term availability of our contents.”</p><p> </p><p>Archiving AMOR’s articles within Portico ensures that the materials published are always available for access. In addition, AMOR’s inclusion in Portico – one of the leading digital preservation services in the world – ensures that AMOR is a step-closer towards its goal of being indexed by PubMed or Medline eventually, as Portico is one of the certified repositories according to Medline’s requirement, Dr. Jong explains.</p><p> </p><p>Meanwhile, Chemical Abstracts Service is an internationally-renowned authority for chemical information that delivers the most complete, cross-linked, and effective digital information for scientific discoveries. CAS, a division of the American Chemical Society, is a source of chemical information and its databases are recognized as the ultimate ‘gold standard’ by the industry. Physically located in Columbus, Ohio, United States, CAS provides updated chemistry content which is maintained by hundreds of PhD scientists from all around the world. The content in CAS covers almost all information and accurate details acquired from thousands of journals, books, patent authorities, web sources, dissertations, conference proceedings, to name a few.</p><p> </p><p>According to Dr. Jong, AMOR is aware that being indexed in relevant databases would broaden its readership and consequently improve the journal’s standing among other oncology journals. “In this regard, we are excited about our inclusion in the CAS databases. This reflects the quality of our published contents and will certainly pave the way for subsequent recognitions by other academic databases,” he says. Dr. Abdel-Rahman goes on to explain, “Our vision for the development and progress of AMOR is to turn it into a benchmark of good quality cancer research and to disseminate this high-quality research to all those who are interested, without any barriers. That is why the indexing and archiving of AMOR into highly accessed biomedical indices is vital to achieve this goal.”</p><p> </p><p>AMOR’s future is bright and hopeful, the EIC says. “We promise our respectable readers and collaborators that AMOR will continue to develop itself and strive to include its contents in other highly accessed biomedical indices,” Dr. Abdel-Rahman concludes. ■</p>


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