The spatial spread of the highly pathogenic avian influenza virus H5N1 and its long-term persistence in Asia have resulted in avian influenza panzootics and enormous economic losses in the poultry sector. However, an understanding of the regional long-distance transmission and seasonal patterns of the virus is still lacking. In this study, we present a phylogeographic approach to reconstruct the viral migration network. We show that within each wild fowl migratory flyway, the timing of H5N1 outbreaks and viral migrations are closely associated, but little viral transmission was observed between the flyways. The bird migration network is shown to better reflect the observed viral gene sequence data than other networks and contributes to seasonal H5N1 epidemics in local regions and its large-scale transmission along flyways. These findings have potentially far-reaching consequences, improving our understanding of how bird migration drives the periodic reemergence of H5N1 in Asia.

Bifidobacteria are well known for their human health-promoting effects and are therefore widely applied in the food industry. Members of the Bifidobacterium genus were first identified from the human gastrointestinal tract and were then found to be widely distributed across various ecological niches. Although the genetic diversity of Bifidobacterium has been determined based on several marker genes or a few genomes, the global diversity and evolution scenario for the entire genus remain unresolved. The present study comparatively analyzed the genomes of 45 type strains. We built a robust genealogy for Bifidobacterium based on 402 core genes and defined its root according to the phylogeny of the tree of bacteria. Our results support that all human isolates are of younger lineages, and although species isolated from bees dominate the more ancient lineages, the bee was not necessarily the original host for bifidobacteria. Moreover, the species isolated from different hosts are enriched with specific gene sets, suggesting host-specific adaptation. Notably, bee-specific genes are strongly associated with respiratory metabolism and are potential in helping those bacteria adapt to the oxygen-rich gut environment in bees. This study provides a snapshot of the genetic diversity and evolution of Bifidobacterium, paving the way for future studies on the taxonomy and functional genomics of the genus.

The meta-QTL and candidate genes will facilitate the elucidation of molecular bases underlying agriculturally important traits and open new avenues for functional markers development and elite alleles introgression in maize breeding program. A large number of QTLs attributed to grain productivity and other agriculturally important traits have been identified and deposited in public repositories. The integration of fruitful QTL becomes a major issue in current plant genomics. To this end, we first collected QTL for six agriculturally important traits in maize, including yield, plant height, ear height, leaf angle, stay-green, and maize rough dwarf disease resistance. The meta-analysis method was then employed to retrieve 113 meta-QTL. Additionally, we also isolated candidate genes for target traits by the bioinformatic technique. Several candidates, including some well-characterized genes, GA3ox2 for plant height, lg1 and lg4 for leaf angle, zfl1 and zfl2 for flowering time, were co-localized with established meta-QTL intervals. Intriguingly, in a relatively narrow meta-QTL region, the maize ortholog of rice yield-related gene GW8/OsSPL16 was believed to be a candidate for yield. Leveraging results presented in this study will provide further insights into the genetic architecture of maize agronomic traits. Moreover, the meta-QTL and candidate genes reported here could be harnessed for the enhancement of stress tolerance and yield performance in maize and translation to other crops.

Colorimetric detection of biogenic amines, well-known indicators of food spoilage, plays an important role for monitoring of food safety. However, common colorimetric sensors for biogenic amines suffer from low color resolution or complicated design and intricate output for the end-users. Herein, we explored a simple but effective strategy for visual monitoring of biogenic amines with multiple color change based on hydrolysis-induced silver metallization reaction to tune the localized surface plasmon resonance (LSPR) adsorption of Au nanorods (NRs). The color change and blue shift of longitudinal LSPR peak of Au NRs were closely related to the concentration of biogenic amines. This strategy provided a simple, sensitive, robust, nondestructive, cost-effective, and user-friendly platform for in situ evaluating the freshness of foodstuffs.

Humans have profoundly affected the ocean environment but little is known about anthropogenic effects on the distribution of microbes. Vibrio parahaemolyticus is found in warm coastal waters and causes gastroenteritis in humans and economically significant disease in shrimps. Based on data from 1103 genomes of environmental and clinical isolates, we show that V. parahaemolyticus is divided into four diverse populations, VppUS1, VppUS2, VppX and VppAsia. The first two are largely restricted to the US and Northern Europe, while the others are found worldwide, with VppAsia making up the great majority of isolates in the seas around Asia. Patterns of diversity within and between the populations are consistent with them having arisen by progressive divergence via genetic drift during geographical isolation. However, we find that there is substantial overlap in their current distribution. These observations can be reconciled without requiring genetic barriers to exchange between populations if long-range dispersal has increased dramatically in the recent past. We found that VppAsia isolates from the US have an average of 1.01% more shared ancestry with VppUS1 and VppUS2 isolates than VppAsia isolates from Asia itself. Based on time calibrated trees of divergence within epidemic lineages, we estimate that recombination affects about 0.017% of the genome per year, implying that the genetic mixture has taken place within the last few decades. These results suggest that human activity, such as shipping, aquatic products trade and increased human migration between continents, are responsible for the change of distribution pattern of this species.

Yersinia pestis is transmitted from fleas to rodents when the bacterium develops an extensive biofilm in the foregut of a flea, starving it into a feeding frenzy, or, alternatively, during a brief period directly after feeding on a bacteremic host. These two transmission modes are in a trade-off regulated by the amount of biofilm produced by the bacterium. Here by investigating 446 global isolated Y. pestis genomes, including 78 newly sequenced isolates sampled over 40 years from a plague focus in China, we provide evidence for strong selection pressures on the RNA polymerase ω-subunit encoding gene rpoZ. We demonstrate that rpoZ variants have an increased rate of biofilm production in vitro, and that they evolve in the ecosystem during colder and drier periods. Our results support the notion that the bacterium is constantly adapting-through extended phenotype changes in the fleas-in response to climate-driven changes in the niche. w | www.nature.com/naturecommunications 1 1234567890():,; † Two small clusters (at CO92 position 2,577,933 and 2,606,316) were excluded as they were the result of copy-number variations in tandem repeat loci * K, the number of variations within a cluster # N, region size of the cluster NATURE COMMUNICATIONS | https://doi.

20Background Humans have profoundly affected the ocean environment but little is known 21 about anthropogenic effects on the distribution of microbes. Vibrio parahaemolyticus is found 22 in warm coastal waters and causes gastroenteritis in humans and economically significant 23 disease in shrimps. 24Results Based on data from 1,103 genomes, we show that V. parahaemolyticus is divided 25 into four diverse populations, VppUS1, VppUS2, VppX and VppAsia. The first two are 26 largely restricted to the US and Northern Europe, while the others are found worldwide, with 27 VppAsia making up the great majority of isolates in the seas around Asia. Patterns of 28 diversity within and between the populations are consistent with them having arisen by 29 progressive divergence via genetic drift during geographical isolation. However, we find that 30 there is substantial overlap in their current distribution. These observations can be reconciled 31 without requiring genetic barriers to exchange between populations if dispersal between 32 oceans has increased dramatically in the recent past. We found that VppAsia isolates from the 33 US have an average of 1.01% more shared ancestry with VppUS1 and VppUS2 isolates than 34 VppAsia isolates from Asia itself. Based on time calibrated trees of divergence within 35 epidemic lineages, we estimate that recombination affects about 0.017% of the genome per 36year, implying that the genetic mixture has taken place within the last few decades. 37Conclusions These results suggest that human activity, such as shipping and aquatic products 38 trade, are responsible for the change of distribution pattern of this marine species. 39 40 Keywords 41 Vibrio parahaemolyticus, population structure, biogeography, anthropogenic change, ocean 42 dispersal 43 44 3 45 Background 46 Hospitable environments for particular marine microbes can be separated by large distances 47 but whether dispersal barriers substantially influence their distribution and evolution is 48 unknown. There are many studies of distribution of marine microbes e.g. [1-4], but these 49 typically survey patterns of macro-scale diversity. Differences in species level or genus level 50 composition between locations are as likely to reflect environmental heterogeneity as 51 dispersal, making the patterns difficult to interpret. Recent spread of microbes between 52 continents has been documented for lineages that cause pathogenic infection of humans, 53 including notorious clonal groups within Vibrio parahaemolyticus and Vibrio cholerae [5-8]. 54 However, these lineages are unusual in using humans as vectors, which might facilitate long-55 range dispersal as in the case of the Haitian cholera outbreak [9]. We currently have little 56 information on rates of spread of the great majority of environmental organisms that do not 57 colonize large-animal hosts. 58 59 V. parahaemolyticus prefers warm coastal waters and causes gastroenteritis in humans [10, 60 11]. Disease outbreaks became common from 1990s and became global, due to spread of 61 pa...

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