Microbial Communities, Metabolites, Fermentation Quality and Aerobic Stability of Whole-Plant Corn Silage Collected from Family Farms in Desert Steppe of North China

Whole-plant corn silages on family farms were sampled in Erdos (S1), Baotou (S2), Ulanqab (S3), and Hohhot (S4) in North China, after 300 d of ensiling. The microbial communities, metabolites, and aerobic stability were assessed. Lactobacillusbuchneri, Acinetobacter johnsonii, and unclassified Novosphingobium were present at greater abundances than others in S2 with greater bacterial diversity and metabolites. Lactobacillus buchneri, Lactobacillus parafarraginis, Lactobacillus kefiri, and unclassified Lactobacillus accounted for 84.5%, and 88.2%, and 98.3% of bacteria in S1, S3, and S4, respectively. The aerobic stability and fungal diversity were greater in S1 and S4 with greater abundances of unclassified Kazachstania, Kazachstania bulderi, Candida xylopsoci, unclassified Cladosporium, Rhizopus microspores, and Candida glabrata than other fungi. The abundances of unclassified Kazachstania in S2 and K. bulderi in S3 were 96.2% and 93.6%, respectively. The main bacterial species in S2 were L. buchneri, A. johnsonii, and unclassified Novosphingobium; Lactobacillus sp. dominated bacterial communities in S1, S3, and S4. The main fungal species in S1 and S4 were unclassified Kazachstania, K. bulderi, C. xylopsoci, unclassified Cladosporium, R. microspores, and C. glabrata; Kazachstania sp. dominated fungal communities in S2 and S3. The high bacterial diversity aided the accumulation of metabolites, and the broad fungal diversity improved the aerobic stability.

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Condensed Tannins Affect Bacterial and Fungal Microbiomes and Mycotoxin Production during Ensiling and upon Aerobic Exposure

Applied and Environmental Microbiology ◽

10.1128/aem.02274-17 ◽

2017 ◽

Vol 84 (5) ◽

Cited By ~ 11

Author(s):

Kai Peng ◽

Long Jin ◽

Yan D. Niu ◽

Qianqian Huang ◽

Tim A. McAllister ◽

...

Keyword(s):

Lactic Acid ◽

Polyethylene Glycol ◽

Microbial Communities ◽

Bacterial Diversity ◽

Fungal Diversity ◽

Condensed Tannins ◽

Total Volatile ◽

Content Type ◽

Mycotoxin Production ◽

Aerobic Stability

ABSTRACTPurple prairie clover (PPC;Dalea purpureaVent.) containing 84.5 g/kg dry matter (DM) of condensed tannin (CT) was ensiled without (control) or with polyethylene glycol (PEG) for 76 days, followed by 14 days of aerobic exposure. Changes in fermentation characteristics were determined, and the composition of bacterial and fungal communities were assessed using metagenomic sequencing. The addition of polyethylene glycol (PEG) that deactivated CT at ensiling increased (P< 0.05 to ∼0.001) soluble N, nonprotein N, lactic acid, total volatile fatty acids, ammonia N, deoxynivalenol (DON), and ochratoxin A (OTA) but decreased (P< 0.001) pH and water-soluble carbohydrates. The concentrations of DON and OTA increased (P< 0.001) for both silages, with the extent of increase being greater for control than for PEG-treated silage during aerobic exposure. The PEG-treated silage exhibited higher (P< 0.01 to ∼0.001) copy numbers of total bacteria,Lactobacillus, yeasts, and fungi than the control. The addition of PEG decreased (P< 0.01) bacterial diversity during both ensiling and aerobic exposure, whereas it increased (P< 0.05) fungal diversity during aerobic exposure. The addition of PEG at ensiling increased (P< 0.05) the abundances ofLactobacillusandPediococcusspecies but decreased (P< 0.01) the abundances ofLactococcusandLeuconostocspecies. Filamentous fungi were found in the microbiome at ensiling and after aerobic exposure, whereasBacillusspp. were the dominate bacteria after aerobic exposure. In conclusion, CT decreased protein degradation and improved the aerobic stability of silage. These desirable outcomes likely reflect the ability of PPC CT to inhibit those microorganisms involved in lowering silage quality and in the production of mycotoxins.IMPORTANCEThe present study reports the effects of condensed tannins on the complex microbial communities involved in ensiling and aerobic exposure of purple prairie clover. This study documents the ability of condensed tannins to lower mycotoxin production and the associated microbiome. Taxonomic bacterial community profiles were dominated byLactobacillalesafter fermentation, with a notable increase inBacillusspp. as a result of aerobic exposure. It is interesting to observe that condensed tannins decreased bacterial diversity during both ensiling and aerobic exposure but increased fungal diversity during aerobic exposure only. The present study indicates that the effects of condensed tannins on microbial communities lead to reduced lactic acid and total volatile fatty acid production, proteolysis, and mycotoxin concentration in the terminal silage and improved aerobic stability. Condensed tannins could be used as an additive to control unfavorable microbial development and maybe enhanced feed safety.

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Effects of a chemical additive on the fermentation, microbial communities, and aerobic stability of corn silage with or without air stress during storage

Journal of Animal Science ◽

10.1093/jas/skaa246 ◽

2020 ◽

Vol 98 (8) ◽

Author(s):

Érica B da Silva ◽

Rebecca M Savage ◽

Amy S Biddle ◽

Stephanie A Polukis ◽

Megan L Smith ◽

...

Keyword(s):

Microbial Communities ◽

Storage Period ◽

Illumina Miseq ◽

Corn Silage ◽

Potassium Sorbate ◽

Chemical Additive ◽

Pichia Kudriavzevii ◽

Aerobic Stability ◽

Whole Plant ◽

Fermentation Profile

Abstract We evaluated the effects of a chemical additive on the microbial communities, fermentation profile, and aerobic stability of whole-plant corn silage with or without air stress during storage. Whole-plant corn was either untreated or treated with a chemical additive containing sodium benzoate, potassium sorbate, and sodium nitrite at 2 or 3 liters/t of fresh forage weight. Ten individually treated and replicated silos (7.5 liters) were made for each treatment. Half of the silos remained sealed throughout a 63-d storage period, and the other half was subjected to air stress for 2 h/wk. The composition of the bacterial and fungal communities of fresh forage and silages untreated or treated with 2 liters/t of fresh forage weight was analyzed by Illumina Miseq sequencing. Treated silage had greater (P < 0.05) aerobic stability than untreated, even when subjected to air stress during storage, but the numbers of yeasts culturable on selective agar were not affected. However, the additive reduced the relative abundance (RA) of the lactating-assimilating yeast Candida tropicalis (P < 0.01). In air-stressed silages, untreated silage had a greater (P < 0.05) RA of Pichia kudriavzevii (also a lactate assimilator) than treated silage, whereas treated silage was dominated by Candida humilis, which is usually unable to assimilate lactate or assimilates it slowly. The additive improved the aerobic stability by specifically preventing the dominance of yeast species that can consume lactate and initiate aerobic spoilage. To the best of our knowledge, this is the first work that identifies the specific action of this additive on shifting the microbial communities in corn silage.

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Temporal Microbial Community Dynamics Within a Unique Acid Saline Lake

Frontiers in Microbiology ◽

10.3389/fmicb.2021.649594 ◽

2021 ◽

Vol 12 ◽

Author(s):

Noor-Ul-Huda Ghori ◽

Michael J. Wise ◽

Andrew S. Whiteley

Keyword(s):

Microbial Community ◽

Environmental Conditions ◽

Fungal Diversity ◽

Community Dynamics ◽

Bacterial Species ◽

Amplicon Sequencing ◽

Fungal Species ◽

Hypersaline Lake ◽

Microbial Community Dynamics ◽

Abundance And Diversity

Lake Magic is an extremely acidic, hypersaline lake found in Western Australia, with the highest concentrations of aluminum and silica in the world. Previous studies of Lake Magic diversity have revealed that the lake hosts acid- and halotolerant bacterial and fungal species. However, they have not canvassed microbial population dynamics across flooding, evapo-concentration and desiccation stages. In this study, we used amplicon sequencing and potential function prediction on sediment and salt mat samples. We observed that the bacterial and fungal diversity in Lake Magic is strongly driven by carbon, temperature, pH and salt concentrations at the different stages of the lake. We also saw that the fungal diversity decreased as the environmental conditions became more extreme. However, prokaryotic diversity was very dynamic and bacteria dominated archaeal species, both in abundance and diversity, perhaps because bacteria better tolerate the extreme variation in conditions. Bacterial species diversity was the highest during early flooding stage and decreased during more stressful conditions. We observed an increase in acid tolerant and halotolerant species in the sediment, involved in functions such as sulfur and iron metabolism, i.e., species involved in buffering the external environment. Thus, due to activity within the microbial community, the environmental conditions in the sediment do not change to the same degree as conditions in the salt mat, resulting in the sediment becoming a safe haven for microbes, which are able to thrive during the extreme conditions of the evapo-concentration and desiccation stages.

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Gut and oral bacterial diversity of the lizard Diploderma splendidum investigated using metagenomic analysis

10.21203/rs.3.rs-128688/v1 ◽

2020 ◽

Author(s):

Zhige Tian ◽

xiaoliang hu ◽

Dandan Gou ◽

Yayong Wu ◽

Peng Guo

Keyword(s):

Bacterial Community ◽

Oral Cavity ◽

Microbial Communities ◽

Bacterial Diversity ◽

Bacterial Species ◽

Sichuan Province ◽

Metagenomic Analysis ◽

Human Pathogens ◽

Fecal Samples ◽

Insight Into

Abstract Background Gut and oral microbial communities are complex and play a key role in their co-evolution with their hosts. However, little is understood about the bacterial community in lizards. In this study, we first investigated the gut and oral bacterial community in Diploderma splendidum from Sichuan Province, China. Metagenomic analysis of feces and oral cavity samples showed distinct differences between Diploderma splendidum and Liolaemus parvus, and L. ruibali and Phymaturus williamsi species. Results Bacteridetes, Firmicutes, Proteobacteria and Fusobacteria were the most abundant phyla in fecal samples. However, the composition of the gut bacterial community of insectivorous lizards (Diploderma splendidum) exhibited unique abundance of phyla Proteobacteria and Chlamydiae when compared with L. parvus, L. ruibali and P. williamsi. Furthermore, Proteobacteria were abundant in oral cavity samples, followed by Actinobacteria, Chlamydiae and Firmicutes. Most striking was that the phylum Chlamydiae was most common in the oral cavity of Diploderma splendidum, when compared with a carnivorous lizard (Varanus komodoensis). In addition, more than 26 bacterial species were detected in the gut and/or oral cavity that were identified as potential human pathogens. Conclusions In this study, metagenomic analysis was carried out to reveal the gut and oral microbiomes, which brought new insight into the complex bacterial community and ecology in Diploderma splendidum.

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Succession of Microbial Communities of Corn Silage Inoculated with Heterofermentative Lactic Acid Bacteria from Ensiling to Aerobic Exposure

Fermentation ◽

10.3390/fermentation7040258 ◽

2021 ◽

Vol 7 (4) ◽

pp. 258

Author(s):

Hao Guan ◽

Qifan Ran ◽

Haiping Li ◽

Xinquan Zhang

Keyword(s):

Acetic Acid ◽

Lactic Acid ◽

Lactic Acid Bacteria ◽

Microbial Communities ◽

Single Molecule ◽

Corn Silage ◽

Water Control ◽

Silage Fermentation ◽

Aerobic Stability ◽

Whole Plant

To further explore the effects of heterofermentative lactic acid bacteria (LAB) on silage fermentation and aerobic stability, whole-plant corn at around the 1/2 milk-line stage was freshly chopped and ensiled in laboratory silos with deionized water (control), Lactobacillus buchneri (LB), or L. rhamnosus (LR). Each treatment was prepared in triplicate for 3, 14, and 60 d of fermentation, followed by 3 and 7 days of aerobic exposure. The dynamic changes in microbial community were studied by single molecule real-time (SMRT) sequencing. The results showed that the two LAB inoculants altered the microbial communities in different ways. Succession from L. plantarum to L. buchneri and L. rhamnosus was observed in LB- and LR-treated silage, respectively. Both silages improved aerobic stability (82 and 78 h vs. 44 h) by occupying the microbial niche to produce higher levels of acetic acid at terminal fermentation. Because Acetobacter fabarum dominated in the silages after aerobic exposure, beta diversity dramatically decreased. In this study, a. fabarum was reported for the first time in silage and was related to aerobic spoilage. The two heterofermentative LAB produced acetic acid and improved the aerobic stability of the corn silage by occupying the microbial niche at terminal fermentation. Inoculated L. rhamnosus had a greater pH for a longer period of time after opening and less DM loss at day 7.

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Microbial Communities and Physicochemical Characteristics of Traditional Dajiang and Sufu in North China Revealed by High-Throughput Sequencing of 16S rRNA

Frontiers in Microbiology ◽

10.3389/fmicb.2021.665243 ◽

2021 ◽

Vol 12 ◽

Author(s):

Tingting Liang ◽

Xinqiang Xie ◽

Jun Ma ◽

Lei Wu ◽

Yu Xi ◽

...

Keyword(s):

Acetic Acid ◽

Lactic Acid ◽

Microbial Communities ◽

Malic Acid ◽

Bacterial Communities ◽

North China ◽

Bacterial Species ◽

Microbial Community Composition ◽

Microbial Composition ◽

Bacterial Phyla

The process of soybean fermentation has been practiced for more than 3,000 years. Although Dajiang and Sufu are two popular fermented soybean products consumed in North China, limited information is available regarding their microbial composition. Hence, the current study sought to investigate, and compare, the physicochemical indicators and microbial communities of traditional Dajiang and Sufu. Results showed that the titratable acidity (TA), and salinity, as well as the lactic acid, and malic acid contents were significantly higher in Sufu samples compared to Dajiang. Furthermore, Sufu samples contain abundant sucrose and fructose, while the acetic acid content was lower in Sufu compared to Dajiang samples. Moreover, the predominant bacterial phyla in Dajiang and Sufu samples were Firmicutes and Proteobacteria, while the major genera comprise Bacillus, Lactobacillus, Tetragenococcus, and Weissella. Moreover, Dajiang samples also contained abundant Pseudomonas, and Brevundimonas spp., while Halomonas, Staphylococcus, Lysinibacillus, Enterobacter, Streptococcus, Acinetobacter, and Halanaerobium spp. were abundant in Sufu samples. At the species level, Bacillus velezensis, Tetragenococcus halophilus, Lactobacillus rennini, Weissella cibaria, Weissella viridescens, Pseudomonas brenneri, and Lactobacillus acidipiscis represented the major species in Dajiang, while Halomonas sp., Staphylococcus equorum, and Halanaerobium praevalens were the predominant species in Sufu. Acetic acid and sucrose were found to be the primary major physicochemical factor influencing the bacterial communities in Dajiang and Sufu, respectively. Furthermore, Bacillus subtilis is strongly correlated with lactic acid levels, L. acidipiscis is positively correlated with acetic acid levels, while Staphylococcus sciuri and S. equorum are strongly, and positively, correlated with malic acid. Following analysis of carbohydrate and amino acid metabolism in all samples, cysteine and methionine metabolism, as well as fatty acid biosynthesis-related genes are upregulated in Dajiang compared to Sufu samples. However, such as the Staphylococcus, W. viridescens, and P. brenneri, as potentially foodborne pathogens, existed in Dajang and Sufu samples. Cumulatively, these results suggested that Dajiang and Sufu have unique bacterial communities that influence their specific characteristics. Hence, the current study provides insights into the microbial community composition in Dajiang and Sufu samples, which may facilitate the isolation of functional bacterial species suitable for Dajiang and Sufu production, thus improving their production efficiency.

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What's the 'Skinny' on Microbiome? Interplay of Immune Cells, Microbes, and Skin Barrier in Health and Disease

Blood ◽

10.1182/blood.v124.21.sci-46.sci-46 ◽

2014 ◽

Vol 124 (21) ◽

pp. SCI-46-SCI-46

Author(s):

Julie Segre ◽

Heidi Kong ◽

Fabio Candotti ◽

Steven M. Holland ◽

Alexandra F Freeman ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Atopic Dermatitis ◽

Microbial Communities ◽

Primary Immunodeficiency ◽

Fungal Diversity ◽

Bacterial Species ◽

Control Site ◽

Genomic Sequencing ◽

Skin Microbiome ◽

Healthy Controls

Abstract Culture-based methods have been the primary techniques used to study microbes inhabiting humans; however, many species are not successfully grown in culture. We performed high throughput genomic sequencing surveys to investigate the topographical and temporal complexity of skin microbial communities from 20 skin sites in healthy adults. Significant differences were observed in the bacterial species predominating in particular microenvironments: sebaceous, moist, and dry. Surveying fungal diversity with genomic sequencing, we determined that core body and arm sites were dominated by Malassezia fungi, with species-level classifications revealing greater topographical resolution between sites. Three foot sites, plantar heel, toenail, and toeweb, exhibited tremendous fungal diversity. Concurrent analysis of bacterial and fungal communities demonstrated that skin physiological attributes and topography differentially shape these two microbial communities. While activated and shaped by microbiota, little is known of how the human immune system regulates the human microbiome, and in turn, how this can result in a disease phenotype. We describe the microbial characteristics of the skin of primary immunodeficiency (PID) patients who share a common phenotype of skin eczema yet have different syndromes arising from monogenic mutations leading to loss of distinct lymphocytic populations. We surveyed the skin microbiomes of 41 individuals with Hyper IgE, Wiskott-Aldrich, and Dedicator of Cytokinesis 8 syndromes and compared them against classical atopic dermatitis (AD) patients and healthy controls at skin sites characteristically affected by eczema, a control site, and a site of pathogen carriage (nares). We found that primary immunodeficiency increases the permissiveness of skin microbial colonization not observed in healthy controls or AD patients. We observed decreased site specificity and longitudinal stability in the PID patients as well as unique colonization by environmental microbiota very rare in healthy or AD controls. We identified taxa correlated and anti-correlated with clinical metamarkers in the PID patients; while Staphylococcus aureus, a known pathogen, was most strongly correlated with disease severity, other staphylococci such as S. haemolyticus and S. epidermidis were significantly overrepresented in the PID individuals. These data provide the first illustration of how PID affects microbial prevalence, diversity, and dynamics in relation to skin disease, gaining insight into host-microbiome interactions and how environmental microbes can uniquely colonize PID patients. This comprehensive survey of the skin microbiome also provided the foundation for analyzing changes in the microbial community associated with common forms of AD, which affect ~15% of U.S. children and ~2% of adults and is associated with Staphylococcus aureus colonization and infection. We studied 10 children with moderate to severe AD at baseline, flare, and post-flare, and healthy controls. Severity was quantified using scoring atopic dermatitis (SCORAD). Samples were obtained from characteristically affected areas, a control site, and nares. Bacterial diversity was dramatically reduced during flare as compared to post-flare and controls. Our studies provide comprehensive characterization of skin microbes in AD and controls confirm the frequent culture-based isolation of S. aureus in AD flares and represent one of the earliest longitudinal investigations of the skin microbiome in a dermatologic disorder. Disclosures No relevant conflicts of interest to declare.

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DIVERSITY OF CULTURABLE BACTERIAL MICROBIOTA OF THE Eisenia foetida DIGESTIVE TRACT

Revista Fitotecnia Mexicana ◽

10.35196/rfm.2018.3.255-264 ◽

2018 ◽

Vol 41 (3) ◽

pp. 255-264 ◽

Cited By ~ 1

Author(s):

J. Abraham Pérez-Pérez ◽

David Espinosa-Victoria ◽

Hilda V. Silva-Rojas ◽

Lucía López-Reyes

Keyword(s):

Bacterial Diversity ◽

Digestive Tract ◽

Bacterial Species ◽

Brain Heart Infusion ◽

Rrna Gene ◽

Eisenia Foetida ◽

Bacterial Isolates ◽

Bacterial Microbiota ◽

Decomposition Of Organic Matter ◽

Earthworm Gut

Bacteria are an unavoidable component of the natural earthworm diet; thus, bacterial diversity in the earthworm gut is directly linked to decomposition of organic matter and development of the surrounding plants. The aim of this research was to isolate and to identify biochemically and molecularly the culturable bacterial microbiota of the digestive tract of Eisenia foetida. Earthworms were sourced from Instituto de Reconversión Productiva y Bioenergética (IRBIO) and Colegio de Postgraduados (COLPOS), México. Bacterial isolation was carried out on plates of Brain Heart Infusion (BHI) culture medium. Fifty six and 44 bacterial isolates were obtained from IRBIO and COLPOS, respectively. The population was composed of 44 Gram-negative and 56 Gram-positive isolates. Over 50 % of the bacterial isolates were rod-shaped cells. The 16S rRNA gene was sequenced and nine genera were identified in worms from IRBIO (Bacillus, Paenibacillus, Solibacillus, Staphylococcus, Arthrobacter, Pantoea, Stenotrophomonas, Acinetobacter and Aeromonas) and six in worms from COLPOS (Bacillus, Paenibacillus, Stenotrophomonas, Staphylococcus, Acinetobacter and Aeromonas). Bacillus was the predominant genus, with eight and six species in the oligochaetes from IRBIO and COLPOS, respectively. The most represented bacteria in the worms from both sites were Bacillus sp. and B. subtilis. The predominance of Bacillus was probably due to spore formation, a reproductive strategy that ensures survival and dispersion in the soil and oligochaetes digestive tract. The gut of E. foetida not only harbored bacterial species of agronomic importance but also species potentially pathogenic for humans (Staphylococcus warneri, Pantoea agglomerans and Stentrophomonas sp.). The larger bacterial diversity in worms from IRBIO could be due to their feeding on cattle manure, which is a rich source of bacteria.

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Substituted 6,7-dimethoxy-5-oxo-2,3,5,9b-tetrahydrothiazolo[2,3-a]isoindole- 3-1,1-dioxide Derivatives with Antimicrobial Activity and Docking Assisted Prediction of the Mechanism of their Antibacterial and Antifungal Properties

Current Topics in Medicinal Chemistry ◽

10.2174/1568026620666200922114735 ◽

2020 ◽

Vol 20 (29) ◽

pp. 2681-2691

Author(s):

Athina Geronikaki ◽

Victor Kartsev ◽

Phaedra Eleftheriou ◽

Anthi Petrou ◽

Jasmina Glamočlija ◽

...

Keyword(s):

Antimicrobial Activity ◽

Antifungal Activity ◽

Drug Targets ◽

Bacterial Species ◽

Pharmaceutical Research ◽

Docking Studies ◽

Fungal Species ◽

Docking Analysis ◽

E Coli ◽

Antibacterial And Antifungal

Background: Although a great number of the targets of antimicrobial therapy have been achieved, it remains among the first fields of pharmaceutical research, mainly because of the development of resistant strains. Docking analysis may be an important tool in the research for the development of more effective agents against specific drug targets or multi-target agents 1-3. Methods: In the present study, based on docking analysis, ten tetrahydrothiazolo[2,3-a]isoindole derivatives were chosen for the evaluation of the antimicrobial activity. Results: All compounds showed antibacterial activity against eight Gram-positive and Gram-negative bacterial species being, in some cases, more potent than ampicillin and streptomycin against all species. The most sensitive bacteria appeared to be S. aureus and En. Cloacae, while M. flavus, E. coli and P. aeruginosa were the most resistant ones. The compounds were also tested for their antifungal activity against eight fungal species. All compounds exhibited good antifungal activity better than reference drugs bifonazole (1.4 – 41 folds) and ketoconazole (1.1 – 406 folds) against all fungal species. In order to elucidate the mechanism of action, docking studies on different antimicrobial targets were performed. Conclusion: According to docking analysis, the antifungal activity can be explained by the inhibition of the CYP51 enzyme for most compounds with a better correlation of the results obtained for the P.v.c. strain (linear regression between estimated binding Energy and log(1/MIC) with R 2 =0.867 and p=0.000091 or R 2 = 0.924, p= 0.000036, when compound 3 is excluded.

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Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome

Microbiome ◽

10.1186/s40168-020-00981-z ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Hannes Petruschke ◽

Christian Schori ◽

Sebastian Canzler ◽

Sarah Riesbeck ◽

Anja Poehlein ◽

...

Keyword(s):

Microbial Communities ◽

Intestinal Microbiota ◽

De Novo ◽

Bacterial Species ◽

Intestinal Microbiome ◽

Single Strain ◽

Small Proteins ◽

Human Intestinal Microbiota ◽

Wide Range

Abstract Background The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. Results We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. Conclusions We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract.

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