A genome and gene catalog of glacier microbiomes

Liu, Yongqin; Ji, Mukan; Yu, Tao; Zaugg, Julian; Anesio, Alexandre M.; Zhang, Zhihao; Hu, Songnian; Hugenholtz, Philip; Liu, Keshao; Liu, Pengfei; Chen, Yuying; Luo, Yingfeng; Yao, Tandong

doi:10.1038/s41587-022-01367-2

Cited by 80 publications

(80 citation statements)

References 67 publications

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“…Some microorganisms still could adapt to these extreme conditions including low temperatures, high levels of solar radiation, periodic freeze–thaw cycles, and nutrient limitations. Liu et al (2022) reported that nearly 1,000 microbe species were discovered in ‘extreme’ Tibetan glaciers, and 82% of the genomes were novel species.…”

Section: Discussionmentioning

confidence: 99%

The microbial communities and natural fermentation quality of ensiling oat (Avena sativa L.) harvest from different elevations on the Qinghai-Tibet Plateau

Bao

Yangzong²,

Yuan³

et al. 2023

Front. Microbiol.

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IntroductionEnsiling whole-crop oat (Avena sativa L.) has attracted a growing interest in the Qinghai-Tibet Plateau. The study aimed to investigate the microbial community and chemical composition of fresh and ensiling oat harvested from six different elevations of the Qinghai-Tibet Plateau.MethodThe oat (A. sativa L. cv. Qingyin No. 1) was planted in six different sites across Qinghai-Tibet Plateau (BM, Bomi County; BY, Bayi County; DZ, Dazi County; BR, Biru County; SC, Suo County; SN, Seni County), where the elevations were in the range of 2,800–4,500 m above sea level (a. s. l.). Oat was harvested at the milk stage and ensiled for 90 days.ResultsThe highest crude protein (CP) and lowest water-soluble carbohydrate (WSC) were observed in fresh oat of SN and BM, respectively, however, no distinct gradient trend in WSC and CP concentrations along the elevation gradient. The lowest LAB counts in fresh oat from the highest elevational regions of SN. After 90 days of ensiling, the pH in all oat silages was lower than 4.2, and silages from SC and SN showed a lower pH and butyric acid concentration, and higher lactic acid (LA) concentration than silages of other regions. The oat silage from BR showed the lowest LA concentration and the highest pH. The bimodal distributions of fungal and bacterial richness in fresh oat along the elevation gradient were observed, while the elevation gradients did not affect the fungal Shannon index in fresh oat. Dioszegia, Cladosporium, and Vishniacozyma were the prevalent fungal genus in fresh oat, while Wickerhamomyces, Candida, and Saccharomyces dominated the fungal communities of silages. Wickerhamomyces and Candida were the dominant genera in oat silages from BM and SC, respectively. Erwinia, Paenibacillus, Pseudomonas, Leuconostoc, and Exiguobacterium dominated the bacterial community of fresh oat, while Lactobacillus and Kosakonia were the dominant bacterial genus in oat silages. Pantoea was the most dominant bacterial genus in fresh oat from low-elevational regions (BM, BY, and DZ). Oat from SN exhibited the best fermentation quality although fresh oat of SN hosted the lowest LAB counts, indicating that high-efficient LAB might be present in fresh oat sampled from high altitudes.

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Section: Discussionmentioning

confidence: 99%

The microbial communities and natural fermentation quality of ensiling oat (Avena sativa L.) harvest from different elevations on the Qinghai-Tibet Plateau

Bao

Yangzong²,

Yuan³

et al. 2023

Front. Microbiol.

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“…This review has attempted to frame pathogen interference within a wider complex system context explored in previous papers [ 1 , 2 , 3 ]. Regarding the number of detected human pathogens we note that global warming induced melting of glaciers is releasing hundreds of new species of ancient pathogens [ 318 ]. Sampling of 21 Tibetan glaciers identified 968 candidate new species of unknown clinical significance [ 318 ].…”

Section: Discussionmentioning

confidence: 99%

“…Regarding the number of detected human pathogens we note that global warming induced melting of glaciers is releasing hundreds of new species of ancient pathogens [ 318 ]. Sampling of 21 Tibetan glaciers identified 968 candidate new species of unknown clinical significance [ 318 ]. Other areas where current knowledge is limited have been highlighted, which includes how influenza vaccination can act to alter the pathogen balance.…”

Section: Discussionmentioning

confidence: 99%

Roles for Pathogen Interference in Influenza Vaccination, with Implications to Vaccine Effectiveness (VE) and Attribution of Influenza Deaths

Jones¹,

Ponomarenko

2022

Infectious Disease Reports

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Pathogen interference is the ability of one pathogen to alter the course and clinical outcomes of infection by another. With up to 3000 species of human pathogens the potential combinations are vast. These combinations operate within further immune complexity induced by infection with multiple persistent pathogens, and by the role which the human microbiome plays in maintaining health, immune function, and resistance to infection. All the above are further complicated by malnutrition in children and the elderly. Influenza vaccination offers a measure of protection for elderly individuals subsequently infected with influenza. However, all vaccines induce both specific and non-specific effects. The specific effects involve stimulation of humoral and cellular immunity, while the nonspecific effects are far more nuanced including changes in gene expression patterns and production of small RNAs which contribute to pathogen interference. Little is known about the outcomes of vaccinated elderly not subsequently infected with influenza but infected with multiple other non-influenza winter pathogens. In this review we propose that in certain years the specific antigen mix in the seasonal influenza vaccine inadvertently increases the risk of infection from other non-influenza pathogens. The possibility that vaccination could upset the pathogen balance, and that the timing of vaccination relative to the pathogen balance was critical to success, was proposed in 2010 but was seemingly ignored. Persons vaccinated early in the winter are more likely to experience higher pathogen interference. Implications to the estimation of vaccine effectiveness and influenza deaths are discussed.

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“…It shows that species diversity is negatively correlated with latitude because latitudinal spatial variation in biotic and abiotic conditions leads to changes in spatial selective pressures ( Gaston, 2007 ). Low-latitude hosts may make high gut microbial diversity increase metagenomic diversity to increase fitness ( Liu et al, 2022 ). High-latitudes hosts may select low gut microbial diversity in order for specific microbes to buffer the abiotic pressures ( Pugnaire et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Geographical patterns of Fejervarya limnocharis gut microbiota by latitude along mainland China’s coastline

Zhao

Ma²,

Jiang³

et al. 2022

Front. Microbiol.

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The gut microbiota affects many aspects of host biology and plays key roles in the coevolutionary association with its host. Geographical gradients may play a certain role on gut microbiota variation in the natural environment. However, the distribution pattern of amphibian gut microbiota in the latitudinal gradient remains largely unexplored. Here, we sampled six natural populations of Fejervarya limnocharis along the eastern coastline of mainland China (spanning 20°–30° N = 1,300 km) using 16S rRNA amplicon sequencing to characterize the gut microbiota. First of all, a significant correlation between gut microbial diversity and latitude was observed in our research system. Second, we discovered that latitude influenced the composition of the gut microbiota of F. limnocharis. Finally, we detected that geographical distance could not determine gut microbiota composition in F. limnocharis. These results indicate that latitude can play an important role in shaping the gut microbial diversity of amphibian. Our study offers the first evidence that gut microbial diversity of amphibian presents a latitudinal pattern and highlights the need for increased numbers of individuals to be sampled during microbiome studies in wild populations along environmental gradients.

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A genome and gene catalog of glacier microbiomes

Cited by 80 publications

References 67 publications

The microbial communities and natural fermentation quality of ensiling oat (Avena sativa L.) harvest from different elevations on the Qinghai-Tibet Plateau

The microbial communities and natural fermentation quality of ensiling oat (Avena sativa L.) harvest from different elevations on the Qinghai-Tibet Plateau

Roles for Pathogen Interference in Influenza Vaccination, with Implications to Vaccine Effectiveness (VE) and Attribution of Influenza Deaths

Geographical patterns of Fejervarya limnocharis gut microbiota by latitude along mainland China’s coastline

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